Apparatuses and methods for sample-specific self-configuration

ABSTRACT

Embodiments in accordance with the present disclosure are directed to configuring an analyzer apparatus for processing a particular sample-processing cartridge. The analyzer apparatus includes a portable container and sample-specific configuration circuitry. The portable container supports and integrates a sample-processing cartridge and the sample-specific configuration circuitry. The sample-specific configuration circuitry identifies configuration information specific to the sample-processing cartridge and configures the analyzer apparatus for a series of state configurations. The configuration can be performed by selecting which of a plurality of biological-sample stimulators to interact with the biological sample, identifying positions in the portable container for each of the selected ones of the plurality of biological-sample stimulators at different times, and while the selected ones of the plurality of biological-sample stimulators are in the identified positions, causing the interactions between the selected ones of the plurality of biological-sample stimulators and the biological sample.

OVERVIEW

Various embodiments in accordance with the present disclosure aredirected to sample-specific self-configuration of an analyzer apparatus.In specific embodiments, the analyzer apparatus self-configures itselffor processing many different sample-processing cartridges, havingdifferent configurations including different biochemical processes,different orders, and/or locations of the biochemical processes, anddifferent parameters for performing the respective biochemicalprocesses.

It can be advantageous for diagnosis of diseases or physiologicalconditions, as well as other analytic purposes, to analyze a biologicalsample to inform clinical decision making. Different types of biologicalsamples and/or analysis use different biochemical processes, differentorders of biochemical processes, and/or involve different parameters.Sample-processing cartridges, such as microfluidic chips, are used forprocessing the biological sample and include different biochemicalprocessing modules and at different locations depending on theparticular biochemical processes to be performed. In accordance withvarious embodiments, an analyzer apparatus is self-configurable for aplurality of different types of biological samples, and which allows forthe analyzer apparatus to be used for a variety of different analysesand processes. The analyzer apparatus is flexible in a distributedsetting that allows for the variety of analyses, while mitigating manualconfiguration by a user, such as a laboratory technician. Theself-configurability of the analyzer apparatus allows for differentdiagnostic and/or processing workflows to be operated by minimallytrained users at the point of biological specimen collection from apatient. For example, the self-configuration allows for processingdifferent subsets of biological processes and different orders ofbiological processes from sample to sample. In specific embodiments, asingle analyzer apparatus is used to perform genomic deoxyribonucleicacid (DNA) diagnostics, cell free DNA (cfDNA) diagnostics, messengerribonucleic acid (mRNA) diagnostics, microRNA (miRNA) diagnostics, andother nucleic acid based tests. In some specific implementations,non-nucleic acid tests are converted to a nucleic acid readout andanalyzed. For example, synthetic DNA coupled to an antibody is used as areadout for antibody protein interactions.

In a number of embodiments, the analyzer apparatus includes a portablecontainer and sample-specific configuration circuitry. The portablecontainer supports and integrates (removably) the sample-processingcartridge and the sample-specific configuration circuitry. Thesample-processing cartridge includes a board assembly with fluidchambers and channels for processing a biological sample therein. Thesample-specific configuration circuitry causes interactions with thebiological sample. For example, the sample-specific configurationcircuitry (or another component of the analyzer apparatus) includes amemory circuit used to store and access configuration informationspecific to the sample-processing cartridge and a configurationprocessing circuit used to configure the analyzer apparatus for a seriesof state configurations. The configuration information can be accessedand/or stored in the memory circuit internal to the analyzer apparatusprior to processing (or starting the process thereof) the biologicalsample. In other specific embodiments, the analyzer apparatus can accessand/or store the configuration information during the analysis, such asin a step-by-step download process (e.g., on-the-fly and during theprocessing), as further described herein.

Configuring the analyzer apparatus for the series of stateconfigurations, in accordance with various embodiments, includesselecting which of a plurality of biological-sample stimulators tointeract with the biological sample, and identifying positions in theportable container for each of the selected ones of the plurality ofbiological-sample stimulators at different times. Configuring theanalyzer apparatus for the series of state configurations furtherincludes, while the each of the selected ones of the plurality ofbiological-sample stimulators are in the identified positions at thedifferent times, causing the interactions between the selected ones ofthe plurality of biological-sample stimulators and the biologicalsample. For example, the analyzer apparatus can include the plurality ofbiological-sample stimulators. Each of the plurality ofbiological-sample stimulators includes or is an energy emitter thatprovides at least one type of energy output and transmits the energyoutput toward the biological sample, thereby causing the interactionwith the biological sample. Example energy outputs includes electricalsignals, optical signals, acoustic and/or ultrasound signals, thermalenergy or transfer of thermal energy (e.g., heating and cooling),magnetic fields or energy, ionizing radiation, pressure, and other typesof outputs.

The biological-sample stimulators include different hardware components.Example biological-sample stimulators include a pneumatic stimulator, agantry (or other mechanical stimulator), an optical stimulator, athermal energy tool, and an electrical stimulator. Although the varioushardware components are described as “a stimulator,” one or more of thestimulators, or components thereof, can be portions of anotherstimulator. In a number of specific embodiments, as further describedherein, the biological-sample stimulators can include subassemblies ofthe analyzer apparatus. In specific embodiments, the pneumaticstimulator includes a pump, tubing and channels that sends forces towardthe biological sample and thereby controls movement of the biologicalsample through the sample-processing cartridge. For example, thepneumatic stimulator constantly controls movement of the biologicalsample through the sample-processing cartridge based on theconfiguration information. In various instances during the analysis, thepneumatic stimulator can cause turbulence for mixing fluids together.The gantry selectively provides a plurality of interactions with thebiological sample at a plurality of locations and based on the series ofstate configurations. In further specific aspects, gantry and aplurality of interface tools coupled to the gantry selectively outputdifferent types of energy outputs toward the biological sample toprovide the different interactions with the biological sample at aplurality of locations across the analyzer apparatus, such as allowingfor movement of interface tools to any location within the analyzerapparatus. Such interface tools can include a magnetic tool, a thermalenergy tool, an acoustic tool, an optical tool, etc. A thermal energytool includes a heat source and/or a cooling source and is used totransfer thermal energy from one medium to another for the purposes ofheating and/or cooling. In some specific examples, the thermal energytool is a radiator, a heat exchanger, and/or a heat sink, althoughembodiments are not so limited. As an example, the thermal energy tooloutputs thermal energy toward the biological sample and thereby providestemperature control at specific locations and time. The thermal energytool can be part of the gantry, in some specific aspects. The electricalstimulator, which includes circuitry, outputs timing signals forcontrolling actions performed by other of the plurality ofbiological-sample stimulators, such as controlling timing of the otherbiological-sample stimulators and processing image data of thebiological sample to provide analytic results. In other specific aspectsuseful with the above-noted embodiments, the optical stimulator, whichincludes a light source and detector circuitry, outputs an opticalsignal toward the biological sample and captures image data of thebiological sample responsive to the optical signal.

In specific embodiments, the sample-specific configuration circuitryfurther includes identification circuit. The identification circuitidentifies the sample-processing cartridge using data located on thesample-processing cartridge and identifies the configuration informationusing the data. The data can include a barcode, such as a matrix barcode, a radio frequency tag, or a memory location, such as a cloud-basedlocation or memory location internal to the analyzer apparatus. In someembodiments, the data includes the configuration information and/or caninstruct how to obtain the configuration information. For example, thesample-specific configuration circuitry can include a communicationcircuit used to download the configuration information from the memorylocation. The configuration information is stored on a memory circuit ofthe sample-specific configuration circuitry (e.g., either prior to theidentification or responsive to a download from an external memorylocation). In accordance with such specific embodiments, theconfiguration processing circuit processes the configuration informationaccessed from the memory circuit and provides the series of stateconfigurations using the processed configuration information.

Configuring the analyzer apparatus for the series of stateconfigurations can include providing spatial location information ofspecific biochemical processing modules self-contained in thesample-processing cartridge along with timing information andidentification of the selected biological-sample stimulators used forperforming the analysis and at the different times. In various specificaspects, the sample-specific configuration circuitry instructs theselected biological-sample stimulators to interface with specificbiochemical processing modules of the sample-processing cartridge basedon parameters identified by the configuration information. Theparameters include spatial locations of the biochemical processingmodules, the selected biological-sample stimulators used to interfacewith the biochemical processing modules, corresponding times for theinterface, and interface parameters indicative of the interactions withthe biological sample. In more-specific embodiments, the parametersinclude specific instructions for the biological-sample stimulatorsinterfacing with the biochemical processing modules including timerequirements of the interaction, two-dimensional or three-dimensionallocations within the sample-processing cartridge for the interface,interface parameters indicative of the interactions with the biologicalsample, which are sometimes herein referred to as “interfaceparameters”. Example interface parameters include exposure time,exposure laser power and duration, stringency temperature, movement offluid in the sample-processing cartridge, temperature and duration oftemperature at particular times, volumes delivered, pressure, flow rate,identification of selected biological-sample stimulators and theinteractions, voltage and current requirements for required forces,laser power, and various combinations thereof.

Various aspects of the present disclosure are directed to methods ofself-configuring an analyzer apparatus. For example, the analyzerapparatus in accordance with the above-noted embodiments is configuredfor performing a particular process on a biological sample. The methodincludes providing a sample-processing cartridge comprising a boardassembly with fluid chambers, channels and a biological sample thereinto a portable container of an analyzer apparatus. The method furtherincludes using sample-specific configuration circuitry to identifyconfiguration information specific to the sample-processing cartridge byscanning a location of the sample-processing cartridge for dataindicative of the configuration information, and configuring theanalyzer apparatus for a series of state configurations for performingthe process on the biological sample using the configurationinformation. Configuring the analyzer apparatus for the series of stateconfigurations includes selecting which of a plurality ofbiological-sample stimulators of the analyzer apparatus interact withthe biological sample at different times specific to an analysis of thebiological sample, identifying positions in the portable container foreach of the selected ones of the plurality of biological-samplestimulators at the different times, and while the selected ones of theplurality of biological-sample stimulators are in the identifiedpositions at the different times, causing interaction between theselected ones of the plurality of biological-sample stimulators and thebiological sample.

Other example aspects are directed to a gantry apparatus that isconfigured to interact with a sample-processing cartridges containing abiological sample. The gantry apparatus includes a set of tracks, abridge framework, and a gantry head. The set of tracks are arrangedparallel to one another and elongates in a first direction. The bridgeframework spans the set of tracks and is configured to travel along theset of tracks in the first direction. The gantry head is supported bybridge framework and is configured to travel in a second direction thatis perpendicular to the first direction and along the bridge framework.The gantry head includes a plurality of interface tools arranged on thegantry head and that can be used to selectively provide the plurality ofinteractions with a biological sample at a plurality of locations. Forexample, the gantry head can physically move to different locationsbetween and outside of the set of tracks in two-dimensional orthree-dimensional directions.

In other specific aspects useful with the above-noted embodiments, theplurality of interface tools are located about or around the peripheryof the gantry head. The gantry head can provide one of the plurality ofinteractions with the biological sample by rotating the gantry head toalign a respective interface tool with a particular location of theplurality of locations. Example interface tools include a heat sourceand/or a cooling source to heat and/or cool the biological sample, amagnetic source to apply magnetic forces, an acoustic tool to applyacoustic forces, a motor, among various other interface tools. Invarious embodiments, the gantry head is detachable from the bridgeframework. For example, the gantry head can be detached from the bridgeframework and another gantry head, which may have a different set ofinterface tools, can be attached to the bridge framework.

Various related and specific aspects are directed to a sample-processingcartridge. In some specific embodiments, the analyzer apparatus includesthe sample-processing cartridge. The sample-processing cartridgeincludes a plurality of biochemical processing modules and the data thatprovides the configuration information. The plurality of biochemicalprocessing modules are self-contained in the board assembly and influidic communication with the fluid chambers and channels. Aspreviously described, the data is located on the sample-processingcartridge which can provide or be used to provide the configurationinformation. For example, the configuration information is specific tothe sample-processing cartridge and used for configuring an analyzerapparatus to perform the biochemical processing using the plurality ofbiochemical processing modules. The data can include a barcode, a radiofrequency tag, and/or a cloud-based location or other memory location.

The above discussion is not intended to describe each embodiment orevery implementation of the present disclosure. The figures and detaileddescription that follow also exemplify various embodiments.

BRIEF DESCRIPTION OF THE FIGURES

Various example embodiments may be more completely understood inconsideration of the following detailed description in connection withthe accompanying drawings in the Appendix, which form part of thispatent document.

FIG. 1 illustrates an example of an analyzer apparatus in accordancewith various embodiments of the present disclosure;

FIG. 2 illustrates an example of an analyzer apparatus in accordancewith various embodiments of the present disclosure;

FIG. 3 illustrates an example of a sample-processing cartridge inaccordance with various embodiments of the present disclosure;

FIG. 4 illustrates examples of layers of a sample-processing cartridgein accordance with various embodiments of the present disclosure;

FIG. 5 illustrates an example method of self-configuring an analyzerapparatus in accordance with various embodiments of the presentdisclosure;

FIG. 6 illustrates another example method of self-configuring ananalyzer apparatus in accordance with various embodiments of the presentdisclosure;

FIGS. 7A-7I illustrates an example gantry apparatus and/or an analyzerapparatus including a gantry in accordance with various embodiments ofthe present disclosure;

FIGS. 8A-8E illustrate examples of sample-processing cartridges, inaccordance with various embodiments of the present disclosure;

FIG. 9 illustrates an example method of using an analyzer apparatus forperforming an analysis on a biological sample, in accordance withvarious embodiments of the present disclosure;

FIG. 10 illustrates an example method of using an analyzer apparatus forperforming an analysis on a sample, in accordance with variousembodiments of the present disclosure;

FIG. 11 illustrates an example method of using an analyzer apparatus forperforming an analysis on a sample, in accordance with variousembodiments of the present disclosure; and

FIG. 12 illustrates a ligase that is active on DNA:RNA hybrid, inaccordance with various embodiments.

While various embodiments discussed herein are amenable to modificationsand alternative forms, aspects thereof have been shown by way of examplein the drawings and will be described in detail. It should beunderstood, however, that the intention is not to limit the invention tothe particular embodiments described. On the contrary, the intention isto cover all modifications, equivalents, and alternatives falling withinthe scope of the disclosure including aspects defined in the claims. Inaddition, the term “example” as used throughout this application is onlyby way of illustration, and not limitation.

DETAILED DESCRIPTION

Embodiments in accordance with the present disclosure are useful forself-configuring an analyzer apparatus for a sample-specific analysis orprocess. In specific aspects, the analyzer apparatus configures itselffor processing a specific sample-processing cartridge, havingbiochemical processing modules at particular locations, based onconfiguration information identified using the sample-processingcartridge. The configuration information identifies a series of stateconfigurations associated with a plurality of biological-samplestimulators of the analyzer apparatus used for performing an analysis ona biological sample within the sample-processing cartridge by causinginteractions with the biological sample. While not necessarily solimited, various aspects of the disclosure may be appreciated through adiscussion of examples in this regard.

Accordingly and in the following description, various specific detailsare set forth to describe specific examples presented herein. It shouldbe apparent to one skilled in the art, however, that one or more otherexamples and/or variations of these examples may be practiced withoutall the specific details given below. In other instances, well knownfeatures have not been described in detail so as not to obscure thedescription of the examples herein. For ease of illustration, the samereference numerals may be used in different diagrams to refer to thesame elements or additional instances of the same element.

Embodiments in accordance with the present disclosure are directed to ananalyzer apparatus that is self-configurable for a plurality ofdifferent types of biological samples, and which can allow for theanalyzer apparatus to be used for a variety of different analyses. Theanalyzer apparatus is flexible in a distributed setting which allows fora variety of analyses while mitigating manual configuration by a user,such as a laboratory technician. A single analyzer apparatus can be usedto perform a variety of processes and analyses on differentsample-processing cartridges having different biochemical processingmodules, at different locations and/or in different orders, and forprocessing different types of biological samples. The analyzer apparatuscan self-configure while in the field (e.g., clinical setting) usingconfigurable hardware that allows for many different combinations ofbiochemical processing in different combinations or orders, volumes,and/or spatial locations of the respective sample-processing cartridge.The analyzer apparatus can be used for providing distributed analysis,such as diagnostics, over a number of different class of applications,including, but not limited to, multiple different infectious diseasetest, genomic tests, and antibody protein interactions. As the analyzerapparatus self-configures, based on data located on the respectivesample-processing cartridge, the apparatus can be used for a variety ofdifferent analysis workflows to be operated by a minimally trained userat the point of biological sample collection from a patient.

In a number of embodiments, the analyzer apparatus includes a portablecontainer and sample-specific configuration circuitry. The portablecontainer supports and integrates a sample-processing cartridge and thesample-specific configuration circuitry. The portable container canremovably integrate different sample-processing cartridges, eachincluding a board assembly with fluid chambers and channels forprocessing a biological sample therein. The sample-specificconfiguration circuitry can identify configuration information specificto a respective sample-processing cartridge and configures the analyzerapparatus for a series of state configurations for performing theprocess on the biological sample. For example, the sample-specificconfiguration circuitry includes a memory circuit and a processingcircuit. The memory circuit stores and/or accesses configurationinformation specific to the sample-processing cartridge. The processingcircuit configures the analyzer apparatus, using the configurationinformation, for a series of state configurations using theconfiguration information.

As further described herein, the configuration information can belocated on the memory circuit internal to the analyzer apparatus, on anexternal memory circuit (and is downloaded and subsequently stored onthe memory circuit of the analyzer apparatus) and/or on thesample-processing cartridge itself. The location can be identified usingdata located on the sample-processing cartridge. The configurationinformation is stored by the analyzer apparatus prior to performing orstarting the process on the biological sample, in some embodiments. As aspecific example, the processing circuit accesses the configurationinformation in a memory location of the memory circuit (internal to theanalyzer apparatus) and then temporarily stores the configurationinformation for accessing during the process, such as cache memoryand/or a volatile memory location. In another specific example, theprocessing circuit accesses the configuration information from anexternal location, such as the cloud, and then temporarily stores theconfiguration information for accessing during the process. Althoughembodiments are not limited to the above examples, and in someinstances, the configuration information is not all accessed and/orinternally stored prior to starting the process on the biologicalsample. In some embodiments, a portion of the configuration informationis stored prior to starting the process, and remaining portion(s) areaccessed and stored during the processing, such as downloadingon-the-fly in which the configuration information for the next step inthe process is accessed and saved while processing a previous step.

The sample-specific configuration circuitry, in a number of embodiments,includes identification circuit and the configuration processingcircuit. The identification circuit identifies the sample-processingcartridge using data located on the sample-processing cartridge andidentify the configuration information using the data. The data caninclude a barcode, such as a matrix barcode, a radio frequency tag, or amemory location (e.g., a memory location of the analyzer apparatus, anexternal circuitry memory location and/or a cloud-based location). Insome specific embodiments, the sample-specific configuration circuitryincludes a communication circuit used to download the configurationinformation from the memory location, such as the cloud-based location,the sample-processing cartridge, or the memory circuit internal to theanalyzer apparatus. The configuration processing circuit furtherprocesses the configuration information accessed from the memory circuitand which provides the series of state configurations using theprocessed configuration information. In various embodiments, thesample-processing cartridge can, itself, include the configurationinformation. As a specific example, the configuration information isstored on a barcode (e.g., a QR code) and read by the identificationcircuit.

Configuring the analyzer apparatus for the series of stateconfigurations includes using the configuration information to selectwhich of a plurality of biological-sample stimulators to interact withthe biological sample, and identify positions in the portable containerfor each of the selected ones of the plurality of biological-samplestimulators at different time. Additionally, the configuration of theseries of state configurations further includes, while the each of theselected ones of the plurality of biological-sample stimulators are inthe identified positions, causing the interactions at the differenttimes, between the selected ones of the plurality of biological-samplestimulators and the biological sample. For example, the analyzerapparatus can include the plurality of biological-sample stimulators.Each of the plurality of biological-sample stimulators is or includes anenergy emitter that provides at least one type of energy output andtransmits the energy output toward the biological sample, therebycausing the interaction with the biological sample. Example energyoutputs includes electrical signals, optical signals, thermal energy ortransfer of thermal energy, sound waves (e.g., acoustic and/orultrasound signals), magnetic fields, ionizing radiation, pressure, andother types of outputs.

Example biological-sample stimulators include a pneumatic stimulator, agantry (or other mechanical stimulator), an optical stimulator, athermal energy tool, and an electrical stimulator. Although the varioushardware components are described as “a stimulator,” one or more of thestimulators, or components thereof, can be portions of anotherstimulator. In a number of specific embodiments, as further describedherein, the biological-sample stimulators can include subassemblies ofthe analyzer apparatus. In specific embodiments, the pneumaticstimulator includes a pump, tubing and channels, and sends forces towardthe biological sample and thereby controls movement of the biologicalsample through the sample-processing cartridge. For example, thepneumatic stimulator constantly controls movement of the biologicalsample through the sample-processing cartridge based on theconfiguration information. In various instances during the analysis, thepneumatic stimulator can cause turbulence for mixing fluids together. Infurther specific aspects, a gantry and a plurality of interface toolscoupled to the gantry selectively output different types of energyoutputs toward the biological sample to provide different interactionswith the biological sample at a plurality of locations across theanalyzer apparatus, such as allowing for movement of interface tools toany location within the analyzer apparatus. A thermal energy tool, whichincludes a heat source and/or a cooling source, outputs thermal energytoward the biological sample or otherwise provides a transfer of thermalenergy to or from the biological sample, and thereby providestemperature control at specific locations and time. The thermal energytool can be part of the gantry, in some specific aspects. And, theelectrical stimulator, which includes circuitry, outputs timing signalsfor controlling actions performed by other of the plurality ofbiological-sample stimulators, such as controlling timing of the otherhardware components and processing image data of the biological sampleto provide analytic results. In other specific aspects useful with theabove-noted embodiments, the optical stimulator, which includes a lightsource and detector circuitry, outputs an optical signal toward thebiological sample and captures image data of the biological sampleresponsive to the optical signal.

The biological-sample stimulators, in specific embodiments, areconfigured for the series of state configurations by the configurationinformation providing spatial location information of specificbiochemical processing modules self-contained in the sample-processingcartridge along with timing information (e.g., the different times) andthe identification of the selected biological-sample stimulators usedfor performing the analysis at the different times. The sample-specificconfiguration circuitry can instruct the selected biological-samplestimulators to interface with the specific biochemical processingmodules of the sample-processing cartridge based on parametersidentified by the configuration information, the parameters includingspatial locations of the biochemical processing modules, the selectedbiological-sample stimulators used to interface with the biochemicalprocessing modules, corresponding times for the interface, and interfaceparameters indicative of the interactions with the biological sample. Inmore specific embodiments, the parameters include specific instructionsfor the biological-sample stimulators interfacing with the biochemicalprocessing modules including time requirements of the interaction,two-dimensional or three-dimensional locations within thesample-processing cartridge for the interface, and values of theinterface that are indicative or associated with the interactions withthe biological sample. Example interface parameters include exposuretime, exposure laser power and duration, stringency temperature,movement of fluid in the sample-processing cartridge, temperature andduration of temperature at particular times, volumes delivered,pressure, flow rate, voltage and current requirements for requiredforces, laser power, and various combinations thereof used forprocessing the biological sample for a specific analysis within thesample-processing cartridge.

Various embodiments of the present disclosure are directed to methods ofself-configuring an analyzer apparatus. For example, the analyzerapparatus, such as that described above, is configured for performing aparticular process on a biological sample. The method can includeproviding a sample-processing cartridge comprising a board assembly withfluid chambers, channels and a biological sample therein to a portablecontainer an analyzer apparatus. The method includes usingsample-specific configuration circuitry to identify configurationinformation specific to the sample-processing cartridge by scanning alocation of the sample-processing cartridge, and configuring theanalyzer apparatus for a series of state configurations for performingthe process on the biological sample using the configurationinformation. Configuring the analyzer apparatus for the series of stateconfigurations includes selecting which of a plurality ofbiological-sample stimulators of the analyzer apparatus interact withthe biological sample at the different times, identifying positions inthe portable container for each of the selected ones of the plurality ofbiological-sample stimulators at the different times, and while theselected ones of the plurality of biological-sample stimulators are inthe identified positions at the different times, causing theinteractions between the selected ones of the plurality ofbiological-sample stimulators and the biological sample.

Other example embodiments are directed to a gantry apparatus that isconfigured to interact with a sample-processing cartridges containing abiological sample. For example, the above-described gantry can include agantry apparatus having a plurality of interface tools. The gantryapparatus includes a set of tracks, a bridge framework, and a gantryhead. The set of tracks are arranged parallel to one another and canelongate in a first direction. The bridge framework spans the set oftracks and is configured to travel along the set of tracks in the firstdirection. The gantry head is supported by bridge framework and isconfigured to travel in a second direction that is perpendicular to thefirst direction and along the bridge framework. The gantry head includesa plurality of interface tools arranged on the gantry head and that areused to selectively provide a plurality of interactions with abiological sample at a plurality of locations within the portablecontainer. For example, the gantry head can physically move to differentlocations between and outside of the set of tracks in two-dimensional orthree-dimensional directions to provide the plurality of interactions,which are identified via the configuration information.

The plurality of interface tools can be located about or around theperiphery of the gantry head. In such embodiments, the gantry headprovides one of the plurality of interactions with the biological sampleby rotating the gantry head to align a respective interface tool with aparticular location of the plurality of locations. Example interfacetools include a heat source and/or a cooling source to heat and/or coolthe biological sample, a magnetic source to apply magnetic forces, anacoustic tool to apply acoustic forces, a motor, among various otherinterface tools. In various embodiments, the gantry head is detachablefrom the bridge framework. For example, the gantry head can be detachedfrom the bridge framework and another gantry head, which may have adifferent set of interface tools, can be attached to the bridgeframework.

Various related embodiments are directed to the sample-processingcartridge. In some specific embodiments, the analyzer apparatus caninclude the sample-processing cartridge. The sample-processing cartridgecan include a plurality of biochemical processing modules and the datathat provides the configuration information. The plurality ofbiochemical processing modules are self-contained in the board assemblyand in fluidic communication with the fluid chambers and channels. Aspreviously described, the data is located on the sample-processingcartridge and used to provide the configuration information. Theconfiguration information is specific to the sample-processing cartridgeand used for configuring an analyzer apparatus to perform thebiochemical processing using the plurality of biochemical processingmodules. The data can include a barcode, a radio frequency tag, and/or acloud-based location or other memory location.

The above-describes apparatus and methods can be used to self-configurean analyzer apparatus, while in the field, for a plurality of differenttypes of biological samples, and which can allow for the analyzerapparatus to be used for a variety of different analysis. Morespecifically, the analyzer apparatus is configured to be flexible in adistributed setting that allows for the variety of analysis, whilemitigating manual configuration by a user, such as a laboratorytechnician. The self-configurability of the analyzer apparatus allowsfor different diagnostic and/or processing workflows to be operated byminimally trained users at the point of biological specimen collectionfrom a patient. The self-configuration can allow for different subsetsof biological processes and different orders of biological processesfrom sample to sample. In specific embodiments, a single analyzerapparatus is used to perform genomic deoxyribonucleic acid (DNA)diagnostics, cell free DNA diagnostics, messenger ribonucleic acid(mRNA) diagnostics, microRNA (miRNA) diagnostics, and other nucleic acidbased tests. In some instances, non-nucleic acid tests can be convertedto a nucleic acid readout and analyzed. For example, synthetic DNAcoupled to an antibody can be used as a readout for antibody proteininteractions.

Turning now to the figures, FIG. 1 illustrates an example of an analyzerapparatus in accordance with various embodiments of the presentdisclosure. The analyzer apparatus 102 can include a portable container105 and sample-specific configuration circuitry 104. The portablecontainer 105 supports and integrates (e.g., accept and hold) asample-processing cartridge 106 and also supports and integrates thesample-specific configuration circuitry 104. The sample-processingcartridge 106, as further illustrated herein, can include a boardassembly with fluid chambers and channels for processing a biologicalsample 108 therein. The portable container 105 receives thesample-processing cartridge 106 and couples to one or more biochemicalprocessing modules of the sample-processing cartridge 106. In specificembodiments, a cartridge assembly or another component can selectivelycause fluidic connection between biochemical processing modules of thesample-processing cartridge 106. For example, the fluidic connection canoccur in response to placing the sample-processing cartridge 106 in theportable container 105 and closing a top (e.g., a lid) of the analyzerapparatus 102, which may cause a biochemical processing module to bepierced (e.g., reagents module) and which results in a fluidicconnection between two or more biochemical processing modules.

A variety of different analyses and processes can be performed on abiological sample or different biological samples using differentsample-processing cartridges. For each respective analysis or process, adifferent sample-processing cartridge is used to perform differentbiochemical processes using different modules and locations of themodules. The analyzer apparatus 102 self-configures to process thedifferent sample-processing cartridges using sample-specificconfiguration circuitry 104. The sample-specific configuration circuitry104 identifies configuration information specific to thesample-processing cartridge 106 and uses the configuration informationto configure the analyzer apparatus 102 for a series of stateconfigurations for performing the process or analysis on the biologicalsample 108. The series of state configurations, as further describedherein, can be associated with the positions of and interactionsprovided by different biological-sample stimulators that are integratedwithin and supported by the portable container 105.

The sample-specific configuration circuitry 104 includes a memorycircuit and a configuration processing circuit. The memory circuit isused to store and access the configuration information specific to thesample-processing cartridge 106. The configuration processing circuitconfigures the analyzer apparatus for the series of state configurationsusing the configuration information. In specific embodiments, thesample-specific configuration circuitry 104 includes identificationcircuit. The identification circuit can identify the sample-processingcartridge 106 using data located on the sample-processing cartridge 106and identify the configuration information using the data. The data caninclude a barcode on the sample-processing cartridge 106, data stored ina radio frequency tag on the sample-processing cartridge 106, and/ordata identifying a memory locations and/or cloud-based location, amongother data. In some embodiments, the analyzer apparatus 102 furtherincludes a communication circuit used to download configurationinformation, such as from a memory location or cloud-based locationidentified using the sample-processing cartridge 106. In variousembodiments, the configuration information is stored on the memorycircuit of the sample-specific configuration circuitry 104, such asprior to the identification or responsive to a download from an externalmemory location.

In various specific embodiments, the configuration information islocated on the sample-processing cartridge (e.g., it is the data), onexternal circuitry, and/or in a memory location internal to the analyzerapparatus (e.g., on the memory circuit). The location can be identifiedfrom or include the data on the sample-processing cartridge, which isidentified by the identification circuit and/or used by thecommunication circuit to access and/or download the configurationinformation. In some embodiments, the configuration information isstored on the memory circuit prior to processing the sample-processingcartridge. For example, the configuration information can be temporarilystored in an easy to locate memory location, such as cache memory. In aspecific embodiment, the analyzer apparatus accesses the configurationinformation in an internal memory location of the analyzer apparatus andthen temporarily stores the configuration information in anotherlocation for accessing during the process, although embodiments are notso limited and the analyzer apparatus can access the configurationwithout storing in the second location. In another specific example, theanalyzer apparatus accesses the configuration information from anexternal location, such as the cloud, and then internally stores theconfiguration information for accessing during the process. As may beappreciated, embodiments are not limited to the above examples, and insome instances, the configuration information is not all accessed and/orinternally stored prior to starting the process on the biologicalsample. As an example, a portion of the configuration information isstored prior to starting the process, and remaining portion(s) areaccessed and stored during the processing, such as downloadingon-the-fly in which configuration information for the next step in theprocess is accessed and saved (temporarily or permanently) whileprocessing the previous step.

As further illustrated herein, such as by FIG. 2, the analyzer apparatus102 includes plurality of biological-sample stimulators that interactphysically with the biological sample. The biological-sample stimulatorsare or include emitters that provide at least one type of energy outputand transmit the energy output toward the biological sample, therebycausing the interactions with the biological sample. Example energyoutputs includes electrical signals, optical signals, thermal energy ortransfer of thermal energy, sound waves (e.g., acoustic and/orultrasound signals), magnetic fields, ionizing radiation, pressure, andother types of outputs.

The sample-specific configuration circuitry 104 can configure at leastsome of the plurality of biological-sample stimulators for the series ofstate configurations. Configuring the analyzer apparatus 102 for theseries of state configurations, in accordance with various embodiments,includes using the configurations information to configure the analyzerapparatus 102 by selecting which of a plurality of biological-samplestimulators to interact with the biological sample at different timesspecific to an analysis of the biological sample, and identifyingpositions in the portable container for each of the selected ones of theplurality of biological-sample stimulators at the different times.Configuring the analyzer apparatus for the series of stateconfigurations further includes, while the each of the selected ones ofthe plurality of biological-sample stimulators are in the identifiedpositions at the different times, causing the interactions between theselected ones of the plurality of biological-sample stimulators and thebiological sample.

Example biological-sample stimulators include a pneumatic stimulator, agantry (or other mechanical stimulator), an optical stimulator, athermal energy tool, and an electrical stimulator, each includedifferent hardware components used to interact with the biologicalsample 108. The analyzer apparatus 102 can include all thebiological-sample stimulators and/or portions that can be removed and/oradded. As a particular non-limiting example, in some implementations, agenomic sample is processed and prepared and later sequenced. In suchimplementations, the optical stimulator may be omitted or otherwise notused.

FIG. 2 illustrates an example of an analyzer apparatus in accordancewith various embodiments of the present disclosure. As illustrates anddescribed above, the analyzer apparatus 210 self-configures forprocessing different sample-processing cartridges using sample-specificconfiguration circuitry 218. The self-configuration can include a seriesof state configurations that describe the states of biological-samplestimulators for a specific duration of time and for differentbiochemical processing.

As illustrated by FIG. 2, the analyzer apparatus 210 can includebiological-sample stimulators, such as a pneumatic stimulator 222, agantry 224, an optical stimulator 212, a thermal stimulator 214, and anelectrical stimulator 220. Although the embodiment of FIG. 2 illustrateseach biological-sample stimulator as a separate stimulator, componentsof or all of the respective stimulator can form part of anotherstimulator. As an example, the thermal stimulator 214, or a componentthereof, can be part of the gantry 224. The difference stimulators canbe also referred to as subassemblies or subsystems (e.g., a pneumaticsubassembly, a mechanical subassembly (e.g., that includes the gantry224), an optical subassembly, a thermal subassembly, and an electricalsubassembly) which are formed of two or more different components, asdescribed herein. Further, each of the stimulators and variouscomponents are supported by and integrated with the portable container216 of the analyzer apparatus 210.

As previously described, the portable container 216 can receive andsecure the sample-processing cartridge. The sample-processing cartridgeincludes a plurality of biochemical processing modules that areself-contained in the board assembly and in fluidic communication withthe fluid chambers and channels. The portable container 216 canintegrate and support the cartridge assembly 215 that includes at leasta cartridge holder that secures the sample-processing cartridges andmechanical couplings that provide connections between thesample-processing cartridge and the biological-sample stimulators of theanalyzer apparatus 210. In some embodiments, the analyzer apparatus 210further includes a cartridge assembly 215. The cartridge assembly 215includes a cartridge holder, a tray motor and a plurality of mechanicalcouplings that provide biological-sample stimulators connections andsample-processing cartridge connections used to couple thesample-processing cartridge with the biological-sample stimulators.Although not illustrated, the analyzer apparatus 210 can include achassis that includes various mounting ports for the biological-samplestimulators, a fan for thermal management, power button(s), and/orstatus lights or other user interfaces.

The pneumatic stimulator 222, which can also be referred to as apneumatic subassembly, can control movement of the biological samplethrough the sample-processing cartridge. For example, the pneumaticstimulator 222 is used to control movement of the biological samplethrough the sample process-cartridge based on the configurationinformation. The movement can change constantly through sampleprocessing. The pneumatic stimulator 222 is configured by theconfiguration processing circuit 221 to deliver volumes, pressures, andflow rates through configurable solenoid valves that enable theprocessing of the biological sample. The pneumatic stimulator 222includes at least a pump, tubing, and channels that are used to sendforces toward the biological sample and thereby control movement of thebiological sample through the sample-processing cartridge. In someinstances, the pneumatic stimulator 222 can also be used to mix reagentsby creating turbulence in modules for mixing. In various embodiments,the pneumatic stimulator 222 includes one or more pumps, solenoids,tubing and channels, an accumulator, and pressure sensors.

The gantry 224 can selectively provide a plurality of interactions witha biological sample across a plurality of locations of the analyzerapparatus 210. In specific embodiments, the gantry can be referred to orform part of a mechanical subassembly or stimulator. The gantry 224 iscoupled to a plurality of interface tools and is used to selectivelyoutput different types of energy outputs toward the biological sample toprovide different interactions with the biological sample at a pluralityof locations across the analyzer apparatus 210. For example, the gantry224 can enable movement of the interface tools to a plurality oflocations, such as any location, within the analyzer apparatus 210. Thegantry 224 can be configured by the configuration processing circuit 221to move various interface tools to the different locations and at thedifferent times for processing the biological sample.

The gantry 224, in specific embodiments and as further illustrated byFIGS. 7A-7E, includes a set of tracks, a bridge framework, and a gantryhead, which are coupled to and enclosed by the analyzer apparatus 210.The set of tracks can be parallel to one another and elongate in a firstdirection, such as along a width or a length of the analyzer apparatus210. The bridge framework spans the set of tracks and can travel alongthe tracks in a first direction that the set of tracks elongate in. Thegantry head is supported by the bridge framework and travels in a seconddirection that is perpendicular to the first direction and along thebridge framework. The gantry head includes the plurality of interfacetools arranged thereon. For example, the plurality of interface toolscan be arranged about or around the periphery of the gantry head. Thegantry head can provide a particular physical interaction with thebiological sample by rotating the gantry head to align a respectiveinteraction tool with a particular location of the plurality oflocations, as further described herein. In specific embodiments, thegantry moves the gantry head to different locations that are between andoutside the set of tracks in two-dimensional and/or three-dimensionaldirections (e.g., X and Y and/or X, Y, and Z) via movement of the bridgeframework and/or gantry head. The different interface tools can includea thermal energy tool to heat or cool the biological sample, a magneticsource to apply magnetic forces, an acoustic tool for applying acoustictools, a motor, and various other interface tools.

As described above, the gantry 224 is used to provide a variety ofinteractions at different locations within the analyzer apparatus 210,which can allow for flexibility for physical interactions (e.g., heat,acoustics, magnetic) with the biological sample. The configurationprocessing circuit 221 can instruct the gantry 224 to provide thedifferent interactions at the different locations and at correspondingtimes during processing of the biological sample. The gantry head can bepre-installed with a fixed set of capabilities, the interface tools canbe detachable and different tools can be attached and/or the gantry headcan be detachable from the bridge framework to provide additional fieldconfigurable capabilities. For example, the gantry head can detach fromthe bridge framework and the bridge framework can be attached to anothergantry head having a different set of interface tools than the gantryhead. In various embodiments, the gantry 224 has a default positionwhich is used to align the gantry 224 and/or the gantry head to thesample-specific cartridge. The default position can include a predefinedlocation (e.g., a home or zero position) in the portable container thatthe gantry 224 moves to or is located in when the analyzer apparatus 210is not processing a cartridge, when a cartridge is first inserted intothe analyzer apparatus, and/or in the event of an error, such as thegantry not aligning with cartridge. In specific embodiments, the defaultpositon can include specific X, Y, and Z coordinate locations.

The thermal stimulator 214, which can also be referred to as a thermalsubassembly, can provide temperature control at specific locations andtime. The thermal stimulator 214, in specific embodiments, is a thermalenergy tool that includes a heat source and/or a cooling source, such asa TEC, and, optionally, a thermistor used to provide the temperaturecontrol. The thermal energy tool uses the heat source and/or coolingsource to output thermal energy toward the biological sample orotherwise provides a transfer of thermal energy from the biologicalsample, and thereby provides temperature control at specific locationsand time. The thermal stimulator 214, or a portion thereof (e.g., theTEC), can be part of the gantry 224, such as an interface tool of thegantry apparatus. The thermal stimulator 214 provides temperaturecontrol at specific locations and times to enable the customized sampleprocessing required by the sample-processing cartridge. The thermalstimulator 214 and/or the thermal energy tool can include a TEC,thermistor, heat sinks, and/or a translation mechanism. In certaininstances, the thermal stimulator 214 can be held in a defined location,but in most cases at least a portion of the thermal stimulator 214 (viathe TEC) is movable by the gantry 224. The configuration processingcircuit 221 provides instructions to the thermal stimulator 214 (e.g.,the thermal energy tool) on the temperature and duration required of thethermal stimulator 214 to accomplish the biological sample processing,while the gantry 224 can be used to locate the specific thermalcomponent at the defined spatial location.

The electrical stimulator 220, which can also be referred to as anelectrical subassembly, can control timing of the otherbiological-sample stimulators. In specific embodiments, the electricalstimulator 220 can be used to process image data for providingdiagnostic results. The electrical stimulator 220 includes circuitryconfigured and arranged to output timing signals for controlling actionsperformed by other of the plurality of biological-sample stimulators.The electrical stimulator 220 can also provide the necessary voltage andcurrent requirements for the gantry 224, optical stimulator 212,pneumatic stimulator 222, and thermal stimulator 214 to provide therequired forces, laser power, pressure or flow rates, and temperaturesas relayed by the sample-processing cartridge through the configurationprocessing circuit 221. The electrical stimulator 220 can include apower source, input/output interfaces, processing circuitry (e.g., acentral processor), a Peripheral Interface Controller (PIC), an analogto digital converter, a data port, among other electrical components.

The optical stimulator 212 can capture image data of the biologicalsample. The optical stimulator 212, which can also be referred to as anoptical subassembly, includes at least a light source and detectorcircuitry used to output an optical signal toward the biological sampleand capture image data of the biological sample responsive to theoptical signal. For example, the sample-processing cartridge can includean assay used for capturing targets, such as specific nucleic acids,antibodies, and/or other targets. The optical stimulator 212 can captureimage data of the targets, which may include fluorescent tags, asfurther described herein. As a specific example, the optical stimulator212 can be used for DNA sequence specific target analysis. The opticalstimulator 212 can include an imaging camera, excitation laser, andoptical relay with the biological sample moved to the optical stimulator212 by the pneumatic stimulator 222 and stringency provided by thethermal stimulator 214. The configuration processing circuit 221provides instructions for the optical stimulator 212 to set the exposuretimes, exposure laser power and duration, stringency temperatures, andspatial location for each sequence specific feature on thesample-processing cartridge. In various embodiments, as furtherdescribed below, the optical stimulator 212 can include a light source(e.g., laser), illumination optics, collection optics, detectorcircuitry, and data transport, among other components.

As a specific example, the optical stimulator 212 includes a lightsource that emits a light beam (e.g., a polarizing light beam), anddetector circuitry. The optical stimulator 212 is configured toselectively optically interrogate a substrate that is part of thesample-processing cartridge, such as an array (e.g., provide the beam oflight to particular locations of the array). For example, the opticalstimulator 212 has a surface adapted to allow placing thereon asubstrate (e.g., a microarray). In other embodiments, the opticalstimulator 212 includes a digital micromirror device (DMP). Further, inspecific embodiments, the optical stimulator 212 includes a mechanicalmechanism, such as a wheel that the digital microarray is placed on thatrotate and/or that rotates the location of the light beam on the digitallight beam. Such a mechanical mechanism can be an interface tool locatedon the gantry head of the gantry, in specific embodiments.

The light beam is selectively directed to particular locations of thesubstrate (e.g., array). For example, the light beam from the lightsource is reflected by the surface to provide an evanescent field over alocation of the substrate such that the location of a substrate in theevanescent field causes a polarization change in the light beam. Theoptical stimulator 212 can include a confocal laser as the light beam.

The detector circuitry detects an optical signal in response to thelight beam being selectively directed to locations of the substrate(e.g., a digital microarray). In specific embodiments, the detectorcircuitry is positioned to detect the polarization change in the lightbeam as the light beam is scanned over the substrate (e.g., amicroarray). The polarization change in the light beam and/or thedetected signal is indicative of the fluorescent signal at theparticular location of the substrate. Processing circuitry is coupled tothe detection circuitry to process an optical signal from the detectioncircuitry to obtain a representation of the fluorescent signal at thelocation of the substrate (e.g., the intensity of the fluorescentsignal). Further, the processing circuitry processes a plurality ofoptical signals to obtain representations of florescent signals at aplurality of locations of the substrate. The detector circuitry caninclude various lenses and/or optical wavelength guides. The opticalstimulator 212, in some instances, is and/or includes imaging circuitry,such as a charged coupled device (CCD).

In various embodiments, the processing circuitry is configured toperform repetitive comparative measurements of the optical signals fromplurality of locations of the substrate (e.g., an array). The processingcircuitry uses the captured optical signals to provide the outputindicative of an analysis performed. Example scanner systems include theTecan™ Power Scanner or the GenePix™ 4000B Microarray Scanner (e.g., amicroarray scanner) and the processing circuitry can utilize variouscomputer-readable medium to analyze the results of the microarray, suchas the Array-Pro™ Analyzer or the GenePix™ Pro Microarray AnalysisSoftware (e.g., Acuity™). The processing circuitry of the opticalstimulator 212, in some specific embodiments, can include a centralprocessor that forms part of the sample-specific configuration circuitry218, the electrical stimulator 220, and/or the optical stimulator 212.

In specific embodiments, the substrate has a plurality of complementarytag sequences at a plurality of different locations on a substrate(e.g., a microarray), which can be referred to as complementary taglocations. The complementary tag sequences are configured to bind todifferent probes. The sample is exposed to the plurality of probes. Forexample, a plurality of sets of different probes can be placed incontact with a biological sample from an organism. Example biologicalsamples include blood, tissue, saliva, urine, etc., taken from anorganism, such as a human.

The detector circuitry scans the substrate, and therefrom, captures thesignals (e.g., optical intensities) indicative of a tag sequence boundto the substrate. The detector circuitry can provide the capturedsignals to the processing circuitry. The processing circuitry uses thecaptured signals, in addition to information indicative of the differentlocations and associated tag sequences, to asses a number of each of thetarget sequences present in the sample. For more specific and generalinformation of example arrays and analysis performed thereon including adigital output technique, reference is made to PCT Application (Ser. No.PCT/US2017/024098), entitled “Apparatuses and Methods for AssessingTarget Sequence Numbers,” filed Mar. 24, 2017 (for example, asillustrated by FIGS. 6 and 7A-7E of the patent document). For morespecific and general information on example sample-processingcartridges, including a modular cartridge that can be configured fordifferent uses, reference is made to U.S. application Ser. No.15/304,030 entitled “Portable Nucleic Acid Analysis System andHigh-Performance Microfluidic Electroactive Polymer Actuators,” filedOct. 13, 2016, each of which are fully incorporated herein by referencefor their teachings (e.g., for example, as illustrated by FIGS. 2A-2C ofthe patent document). Although embodiments are not limited to assessingtarget sequence numbers, and can include a variety of different arraysand assessments.

The various stimulators and/or hardware components illustrated by FIG. 2can interface with one another and/or form part of one another. Forexample, the optical stimulator 212 can interface with the electricalstimulator 220 by the electrical stimulator 220 providing laser power,camera power, and camera communications. The optical stimulator 212 canalso interface with the cartridge assembly 215 by translating to thesubstrate for imaging. The electrical stimulator 220 can additionallyinterface with the thermal stimulator 214 by providing TEC power andthermistor values, with the pneumatic stimulator 222 by providingsolenoid power, pump power, and pressure sensing, and/or with thechassis by providing communication input (e.g., Ethernet input fordownloading data) and power input.

The data located on the sample-processing cartridge is used to providethe configuration information to the analyzer apparatus 210 via thesample-specific configuration circuitry 218. The sample-specificconfiguration circuitry 218 provides the location and requirements ofspecific biological processing modules on the sampled-processingcartridge. The location information can provide the x, y and/or zcoordinate locations of interface features for the gantry 224, thermalstimulator 214, pneumatic stimulator 222, and/or optical stimulator 212to interface with the sample-processing cartridge.

As illustrated, the sample-specific configuration circuitry 218 includesa memory circuit 223, an identification circuit 219 and a configurationprocessing circuit 221. The memory circuit 223 stores and is used toaccess configuration information specific to respectivesample-processing cartridges. The identification circuit 219 canidentify the sample-processing cartridge using the data located on thesample-processing cartridge and identify the configuration informationusing the data. The data can include a barcode, such as matrix barcode(e.g., a quick response (QR) code) located on the sample-processingcartridge scanned by the identification circuit 219, data stored in aradio frequency tag on the sample-processing cartridge and read by theidentification circuit 219, and/or a memory or cloud-based locationprovided by the sample-processing cartridge (such as via a bar code orQR code that identifies the memory or cloud-based location). Theidentification circuit 219 can include components used to scan the code,read the data, and/or the communication circuit to download theconfiguration information from the memory or cloud-based location.

The memory location can include a location on a memory circuit of theanalyzer apparatus 210 (e.g., the memory circuit 223 of thesample-specific configuration circuitry 218), a memory location on anexternal processing circuitry (e.g., external controller incommunication with the analyzer apparatus 210), and/or a cloud-basedlocation. In various specific embodiments, the configuration informationis included in the data on the sample-processing cartridge. In someembodiments, the analyzer apparatus 210 is in communication with anexternal processing circuitry, such as an external controller. Theexternal processing circuitry can include a user interface, a bar codeor radio frequency identification (RFID) reader, and can be incommunication with the analyzer apparatus 210. For example, the externalprocessing circuitry can provide patient information to the analyzerapparatus 210, receive final data from the analyzer apparatus 210 and/oruse the data to generate a report. The external processing circuitry andanalyzer apparatus 210 can communicate wirelessly or in a wired manner(e.g., Ethernet). In other embodiments and/or in addition, the analyzerapparatus 210 includes an RFID reader and/or barcode reader. Theanalyzer apparatus 210 can communicate the data to the externalprocessing circuitry to identify the configuration information and/orcan otherwise use the data to identify the configuration information.For example, the analyzer apparatus 210 can use the data to obtain theconfiguration information, which may be included in the data, or from amemory location external or internal to the analyzer apparatus 210. Theanalyzer apparatus 210 can further be configured to collect image data,analyze the image data, and output an analysis using an internalprocessing circuitry.

The configuration information can be accessed and stored prior toperforming the process on the biological sample, as previously described(although embodiments are not so limited). In some specific embodiments,once an analyzer apparatus accesses and stores, e.g., downloads, theconfiguration information for a first type of test, the configurationinformation is stored on the memory circuit internal to the analyzerapparatus 210 and subsequently used for another sample-processingcartridge to perform the first type of test on a different sample. As aspecific example, a first sample-processing cartridge is inserted intothe analyzer apparatus. The analyzer apparatus identifies that the firstsample-processing cartridge is associated with testing a blood sample ofa human for DNA targets associated with ten different types of cancer.The sample-processing cartridge includes data for identifying the typeof test and/or accessing the configuration information associated withthe test (e.g., internal or external). Subsequent to processing thefirst sample-processing cartridge, a second sample-processing cartridgeis inserted into the analyzer apparatus. The analyzer apparatusidentifies that the second sample-processing cartridge is associatedwith testing a blood sample of another human for DNA targets associatedwith the same ten different types of cancer (e.g., is associated withthe same test as the first sample-processing cartridge). The analyzerapparatus accesses the internal memory location used to store theconfiguration information for the first sample-processing cartridge and,optionally, without accessing or downloading the configurationinformation from an external location. In this manner, the analyzerapparatus can be configured for different tests based onsample-processing cartridges inserted therein, and can store theconfiguration information for subsequent tests. Although embodiments arenot so limited, and can include downloading the configurationinformation for each cartridge.

The configuration information, which can also be referred to as a“configuration file,” can include a series of state configurations thatdescribes the state of all biological-sample stimulators (e.g., hardwarecomponents) for a specific duration of time. The configurationinformation can provide the analyzer apparatus 210 with the spatiallocation of specific biochemical processing modules of sample-processingcartridge along with identification of the selected biological-samplestimulators of the plurality used for performing the analysis and timerequirements (e.g., the different times associated with the spatiallocation and interactions). The configuration processing circuit 221 canprocess the configuration information and provide the series of stateconfigurations. For example, the configuration processing circuit 221can provide the location and requirements of specific biologicalprocessing modules on the sample-processing cartridge. The locationinformation provides the x, y and z coordinate locations of interfacefeatures for the gantry 224, thermal stimulator 214 (e.g., thermalenergy tool), pneumatic stimulator 222, electrical stimulator 220, andoptical stimulator 212 to interface with the sample-processing cartridgeand thereby cause the interaction with the biological sample.

In accordance with various embodiments, the sample-specificconfiguration circuitry 218 can configure the analyzer apparatus 210 forthe series of state configurations by providing spatial locationinformation of specific biochemical processing modules self-contained inthe sample-processing cartridge along with timing information andidentification of the selected biological-sample stimulators of theplurality used for performing the analysis at the different times. Thesample-specific configuration circuitry 218, such as via theconfiguration processing circuit 221, can instruct the selectedbiological-sample stimulators to interface with specific biochemicalprocessing modules of the sample-processing cartridge based onparameters identified by the configuration information. The parameterscan include spatial locations of the biochemical processing modules, theselected biological-sample stimulators used to interface with thebiochemical processing modules, corresponding times for the interfacing,and interface parameters indicative of the interactions with thebiological sample. As specific examples, the parameters include specificinstructions for the selected biological-sample stimulators interfacingwith the biochemical processing modules including time requirements ofthe interface and/or interaction, two-dimensional or three-dimensionallocations within the sample-processing cartridge for the interface, andvalues of the interface (e.g., temperature, magnetic and mixing).

The sample-specific configuration circuitry 218 can thereby configurethe biological-sample stimulators for the series of state configurationsthat are specific to the sample-processing cartridge and based on dataidentified directly from or otherwise associated with thesample-processing cartridge. The series of state configurations includelocations and requirements of specific biological processing modules onthe sample-processing cartridge and parameters for respectivebiological-sample stimulators.

In further embodiments, the analyzer apparatus 210 can include one ormore sensors. The sensors can be used to provide feedback on the statusof the parameters, such as verifying that the correct interaction isoccurring at the correct location and with the correct interface values.In some embodiments, the feedback provided by the sensors may indicatethat the gantry is not properly aligned with the sample-processingcartridge. In such embodiments, the gantry is instructed to return tothe default position to re-align with the sample-processing cartridge.Although embodiments are not so limited and in some specific embodimentsthe sensors are used to adjust the alignment of the gantry withoutreturning to the default position.

Although the above describes the analyzer apparatus 210 self-configuringby identifying data on the sample-processing cartridge, embodiments arenot so limited. For example, the analyzer apparatus 210 canself-configure by a user entering a code into the analyzer apparatus 210and the code identifying the series of state configurations. In otherexample embodiments, a configuration file is uploaded to the analyzerapparatus 210, such as from external processing circuitry.

Further, in various embodiments, the sample-processing cartridge caninclude a means for a user to configure the sample-processing cartridge.For example, the user can mark a step by hand on the sample-processingcartridge, such as a label which is read by the analyzer apparatusand/or manually entered into the sample-processing cartridge by anotheruser. In other embodiments, the specific-instructions are coded into thedata on the sample-processing cartridge that is read by the analyzerapparatus.

FIG. 3 illustrates an example of a sample-processing cartridge inaccordance with various embodiments of the present disclosure. Thesample-processing cartridge 330 can include a board assembly 332, aplurality of biochemical processing modules 333, an input port forreceiving a biological sample 331, and (identification) data 341. Theboard assembly 332 has fluid chambers and channels for processing abiological sample therein. The plurality of biochemical processingmodules 333 are self-contained and/or otherwise coupled to the boardassembly 332 and in fluidic communication with the fluid chambers andchambers.

The data 341 located on the sample-processing cartridge 330 providesconfiguration information specific to the sample-processing cartridgefor configuring an analyzer apparatus to perform the biochemicalprocessing using the plurality of biochemical processing modules 333.The data 341, as described above, can include a barcode, a radiofrequency tag, and/or identification of a cloud-based location or othermemory location, such as a link indicative of the cloud-based locationor other memory location.

The biochemical processing modules 333 are configured to performbiochemical processing on the biological sample 331. Example modules, asillustrated, include a purification module 334, a target selectionmodule 335, an amplification module 337, and a detection module 339.Embodiments are not limited to the specific modules illustrated by FIG.3 and can include a variety of modules for different analysis, asfurther described in connection with FIGS. 8A-8E. The modules canadditionally include a sample collection module used to interface with abiological sample container and/or transfer device, such as a bloodtube, and includes a sample chamber configured to hold a volume of thebiological sample.

In specific embodiments, the purification module 334 can performextraction of targets within the biological sample. For example, thepurification module can mix the sample with enzymes and chemicals torelease the targets from the biological sample. The targets can includeDNA, RNA, and antibodies, among other types of targets. In specificembodiments, the purification module 334 can include a proteinase K (PK)chamber that contains PK, and a TEC interface to allow for engagementwith the TEC. The PK chamber can include other chemicals, such as adetergent and/or salts. The PK chamber is heated, via the TEC, toactivate PK and is mixed with the biological sample to release thetargets (e.g., bound DNA) bound to other components in the biologicalsample (via the pneumatic stimulator). The purification module 334 canfurther perform target isolation, in some embodiments. For example, thepurification module 334 can include binding chamber(s), one or morebinding elements, and the TEC interface. The binding elements caninclude beads or a solid support, such as a silica frit, as furtherdescribed herein. In some embodiments, the purification module 334include two separate modules, e.g., an extraction module and anisolation module, that perform the functions described above.

The target selection module 335 can be used to bind specific targets toprobes. The target selection module 335 can include one or morechambers, probes and enzymes, and a TEC interface. For example, probescan be mixed with the isolated targets from the purification module 334and the targets are annealed to the probes.

The amplification module 337 can be used to amplify the targets bound tothe probes via a PCR process, as further described herein. Theamplification module 337 can include probes, universal PCR primers,enzymes and other reagents, and a TEC interface. In some embodiments,the target selection module 335 and the amplification module 337 includeone module, e.g., a library preparation module that perform thefunctions described above.

The detection module 339 can be used to bind the amplicons to asubstrate and detect the bound amplicons, which include targets bound toprobes, as further described herein. The detection module 339 caninclude a mixing chamber used to prepare a hybridized sample, ahybridization chamber, a microarray or other substrate, and interfacesto various hardware components (e.g., TEC, laser, optics). In variousembodiments, the detection does not occur on the analyzer apparatus, andthe sample-processing cartridge 330 does not include the detectionmodule 339.

The sample-processing cartridge 330 can include various additionalcomponents. For example, the sample-processing cartridge 330 can includea liquid reagents module 338 that contains various reagents used forprocessing the biological sample 331. The liquid reagents module 338 maybe pierced by the analyzer apparatus responsive to placement of thesample-processing cartridge 330 in a cartridge assembly, and whichresults in liquid communications between the liquid reagents module 338and one or more other modules and/or chambers of the board assembly 332.The sample-processing cartridge 330 can additionally include a wastecollection chamber 340 used to collect various fluids and material aftervarious processes.

FIG. 4 illustrates examples layers of a sample-processing cartridge inaccordance with various embodiments of the present disclosure. Asillustrated, the sample processing cartridge 441 can be formed in avariety of layers. The top layer 442 can include the reagents module andother modules, such as various modules that are moved to by the gantry(or other mechanical subassembly) of the analyzer apparatus. The bottomlayer 444 can include remaining modules, such as the substrate (e.g., anarray). And, below the bottom layer 444 can include a laminate layer 446that includes the fluid channels, valves, and vents.

FIG. 5 illustrates an example method of self-configuring an analyzerapparatus in accordance with various embodiments of the presentdisclosure. As described above, prior to processing a biological sample,configuration information is identified and/or loaded into the analyzerapparatus, such as via software or obtained using data on thesample-processing cartridge, and that prescribes the stateconfigurations for each step of the sample processing. The biologicalsample can be processed in a number of different ways depending on thetype of analysis and/or diagnostic assay being run. Sample preparationis accomplished using a variety of different biochemical processes. Aspecific example of biochemical processes that can be run on theanalyzer apparatus are described below and include DNA extraction, DNAisolation, biotinylation, probe annealing, probe extension, universalamplification, and microarray hybridization in some specific embodimentsused for detecting DNA targets.

Example approaches use solid supports (streptavidin biotin binding orDNA binding to silica frits), ligases, terminal transferases, DNApolymerases, RNA reverse transcriptases, uracil DNA glycosylate,exonucleases, DNA probe annealing to templates, and other enzymes. Eachof these biochemical processes can use different reaction volumes,temperatures, times, and (physical) interactions with the biologicalsample. The requirements are not uniform and therefore static locationsof biological-sample stimulators and/or hardware components thereof(e.g. TECs, magnets, and mixers) does not allow for performing multipledifferent workflows. Example configurations of modules for specificdiagnostic testing are shown in FIGS. 10 and 11. These are given asexamples, but other common biological sample processing workflows can beimplemented on the field configurable analyzer apparatus.

The method as illustrated by FIG. 5 can include providing asample-processing cartridge comprising a board assembly with fluidchambers, channels and a biological sample therein. Optionally, in someembodiments (as illustrated by the dashed line), the method can includeformatting a sample-processing cartridge for a specific analysis. Forexample, the type of analysis can be identified, at 551, and asample-processing cartridge can be formatted with particular biochemicalprocessing modules to perform the respective biochemical processes andin the respective order, at 553. Additionally, in some embodiments, datais located on the sample-processing cartridge such that the analyzerapparatus identifies configuration information specific to thesample-processing cartridge without or with minimal user input. In otherembodiments, the sample-processing cartridge can be preconfigured for aspecific analysis. A sample from a patient (e.g., human or otherorganism) can be collected, at 555, and input to an input port of thesample-processing cartridge.

The sample-processing cartridge can be provided to an analyzerapparatus, such as by placing the sample-processing cartridge into acartridge assembly of the analyzer apparatus, at 557. In responsethereto, sample-specific configuration circuitry of the analyzerapparatus can identify configuration information specific to thesample-processing cartridge by scanning a location of thesample-processing cartridge for data. The analyzer apparatus can verifythat the configuration information is identified, at 559. If theconfiguration information is not identified, the analyzer apparatus canoutput a message, such as a message on a user interface of the analyzerapparatus, a message to other circuitry (e.g., external processingcircuitry accessibly by a technician), and/or other indications on theanalyzer apparatus (e.g., buzzing sound or flashing light indicating anerror), at 561.

In response to verification of identified configuration information, theanalyzer apparatus is configured for a series of state configurations toperform the analysis on the biological sample, at 563. As previouslydescribed, configuring the analyzer apparatus for the series of stateconfigurations can include providing spatial location information ofspecific biochemical processing modules self-contained in thesample-processing cartridge along with timing information andidentification of the selected biological-sample stimulators of theplurality used for performing the analysis and at the different times.In specific embodiments, the configuration can include directing ones ofthe selected biological stimulators to interface with the respectivebiochemical processing modules of the sample-processing cartridge atdifferent times during the analysis based on the spatial locations ofthe biochemical processing modules, and interface parameters indicativeor associated with interaction(s) with the biological sample.

FIG. 5 further illustrates an example of a plurality of biochemicalprocesses that the analyzer apparatus is configured for. As illustrated,the biochemical processes can include DNA preparation at 564, librarypreparation at 565, and detection/analysis at 566 and 567. In a specificembodiment, DNA preparation can include DNA extraction and isolation,library preparation can include annealing, ligation, and/or PCR, asfurther described herein.

FIG. 6 illustrates another example method of self-configuring ananalyzer apparatus in accordance with various embodiments of the presentdisclosure. In various embodiments, the analyzer apparatus may beconfigured at manufacturing for particular uses. In such embodiments, adifferent analyzer apparatus is used for different analysis. Asillustrated by the dashed line, the method can optionally includeformatting a sample-processing cartridge for a specific analysis. Forexample, the type of analysis can be identified, at 670, and asample-processing cartridge can be formatted with particular biochemicalprocessing modules to perform the respective biochemical processes andin the respective order, at 671. The analyzer apparatus can beconfigured at manufacturer for the specific analysis, at 672. Theanalysis can include a series of state configurations for selectedbiological-sample stimulators of the analyzer apparatus and at differenttimes, as previously described.

A biological sample from a patient (e.g., human or other organism) canbe collected and input to an input port of the sample-processingcartridge, at 673. The sample-processing cartridge can be provided to ananalyzer apparatus at 674, such as by placing the sample-processingcartridge into a cartridge holder. In response, the analyzer apparatus,using the pre-configured series of state configurations, perform theanalysis on the biological sample. As previously described, configuringthe analyzer apparatus for the series of state configurations canfurther includes providing spatial location information of specificbiochemical processing modules self-contained in the sample-processingcartridge along with timing information and identification of theselected biological-sample stimulators of the plurality used forperforming the analysis and at the different times.

Similarly to FIG. 5, FIG. 6 further illustrates an example of aplurality of biochemical processes that the analyzer apparatus isconfigured for. As illustrated, the biochemical processes can includeDNA preparation at 675, library preparation at 676, anddetection/analysis at 677 and 678. In a specific embodiment, DNApreparation can include DNA extraction and isolation, librarypreparation can include annealing, ligation, PCR, as further describedherein.

FIGS. 7A-7F illustrate example gantry apparatuses and/or analyzerapparatuses including a gantry in accordance with various embodiments ofthe present disclosure. As previously described, various embodiments aredirected to a gantry apparatus such as a gantry and/or an analyzerapparatus that includes a gantry. The gantry can be used to selectivelyprovide a plurality of interactions with a biological sample, ascontained in a sample processing cartridge, across a plurality oflocations of an analyzer apparatus. For example, the gantry includes aplurality of interface tools that selectively output different types ofenergy toward the biological sample to provide different interactionswith the biological sample. The gantry can enable movement of theinterface tools to any location within the analyzer apparatus by movingthe interface tools in an X, Y, and/or Z direction.

FIG. 7A illustrates an example of a gantry apparatus in accordance withvarious embodiments. As illustrated, the gantry apparatus includes a setof tracks 760-1, 760-2, a bridge framework 763, and a gantry head 756.The set of tracks 760-1, 760-2 are arranged parallel to one another andthe bridge framework 763 spans the set of tracks. For example, thebridge framework can be perpendicular to the set of tracks, althoughembodiments are not so limited and the bridge framework can be at avariety of angles to the set of tracks. The gantry, in specificembodiments and as further illustrated herein, is enclosed by theanalyzer apparatus. The set of tracks 760-1, 760-2 can be parallel toone another and elongate in a first direction 762, such as along a widthor a length of the analyzer apparatus. The bridge framework spans theset of tracks in a second direction 764 and can travel along the set oftracks in a first direction 762 that the set of tracks elongate in. Thegantry head 756 is supported by the bridge framework and travels in asecond direction 764 that is perpendicular (or at another angle) to thefirst direction and along the bridge framework. The gantry head 756includes the plurality of interface tools arranged thereon. The gantryhead 756 can provide a particular physical interaction with thebiological sample by rotating the gantry head to align a respectiveinterface tool with a particular location, as further described herein.In specific embodiments, the gantry moves the gantry head 756 todifferent locations that are between and outside the set of tracks intwo-dimensional and/or three-dimensional directions (e.g., X and Yand/or X, Y, and Z) via movement of the bridge framework and/or gantryhead. The different interface tools can include a thermal energy tool toheat or cool the biological sample (e.g., a TEC), a magnetic source toapply magnetic forces, an acoustic tool for applying acoustic tools, amotor, and various other tools.

In accordance with various embodiments, the gantry apparatus can movethe gantry head to different locations using a variety of mechanisms,such as one or more rotors coupled to components of the gantryapparatus. Other mechanisms, as would be appreciated by one of ordinaryskill in the art, can include rotating wheels or other types of rotatingcomponents, gears and/or rotary gear systems, pulleys, crank and shaftsand/or crankshafts and rods, collars, couplings, cams, clutches,flywheels, shaft ends, spindles, meshing gears, and horizontal orvertical shafting, among other types of mechanisms.

FIG. 7B illustrates a more specific example of a gantry apparatus inaccordance with various embodiments. The gantry apparatus includesbrackets 755-1, 755-2 that support the set of tracks and that can bemounted or otherwise coupled to the frame of the portable container ofthe analyzer apparatus. Each of the tracks of the set or at least one ofthe tracks are formed by or include at least one arm (or a set of arms)that is coupled to a rotor 757-1. Rotation of the rotor 757-1 (andoptionally another rotor coupled to the other arm) moves the arm(s)coupled thereto, as well as the bridge framework spanning the set oftracks, in a first direction 761, such as along a width or a length ofthe analyzer apparatus. The bridge framework spans the set of tracks andis configured to travel along the set of tracks in the first direction761 responsive to movement of the rotor 757-1 and the arm coupled to therotor 757-1. A gantry head 756 is supported by the bridge framework andis configured to travel in a second direction 759 that is perpendicularto the first direction 761 and along the bridge framework. For example,another rotor 757-2 is coupled to the bridge framework. Rotation of theother rotor 757-2 moves the gantry head 756 in a direction perpendicularto the set of tracks. The bridge framework can include at least one armthat is coupled to the other rotor 757-2 and the gantry head 756 tocause movement of the gantry head 756 in the direction perpendicular tothe set of track, e.g., the second direction 759.

As further illustrated and described herein, the gantry head 756includes plurality of interface tools arranged on the gantry head andthat are used to selectively provide a plurality of interactions with abiological sample at a plurality of locations within the portablecontainer of the analyzer apparatus. The gantry head 756 can physicallymove to different locations between and outside of the set of tracks intwo-dimensional or three-dimensional directions to provide the pluralityof interactions, which are identified via the configuration information.In specific embodiments, the gantry can be referred to or form part of amechanical subassembly or stimulator. The gantry, via the plurality ofinterface tools coupled thereto, is used to selectively output differenttypes of energy outputs toward the biological sample to providedifferent interactions with the biological sample at a plurality oflocations across the analyzer apparatus.

FIG. 7C illustrates a view of the gantry head of the gantry apparatus inaccordance with various embodiments. The plurality of interface toolscan be located about or around the periphery of the gantry head, such aslocated on the circumference of the gantry head. In such embodiments,the gantry head is rotatable, e.g., a rotating head, and used to provideone of the plurality of interactions with the biological sample byrotating the gantry head to align a respective interface tool with aparticular location within the analyzer apparatus. As described above,example interface tools that can be coupled to the gantry head caninclude a heat source and/or a cooling source (e.g., TEC) to heat and/orcool the biological sample, a magnetic source to apply magnetic forces,an acoustic tool to apply acoustic forces, a motor, among various othertools. In various embodiments, the gantry head is detachable from thebridge framework. For example, the gantry head can be detached from thebridge framework and another gantry head, which may have a different setof interface tools, can be attached to the bridge framework.

FIG. 7D illustrates an example of an analyzer apparatus that includes agantry. As described above, the gantry can be enclosed by the analyzerapparatus. The gantry is used to provide a variety of interactions atdifferent locations within the analyzer apparatus, which can allow forflexibility for physical interactions (e.g., heat, acoustics, magnetic)with the biological sample. The configuration processing circuit caninstruct the gantry to provide the different interactions at thedifferent locations and at corresponding times during processing of thebiological sample. The gantry head can be pre-installed with a fixed setof capabilities, the interface tools can be detachable and differenttools can be attached and/or the gantry head can be detachable from thebridge framework to provide additional field configurable capabilities.

As illustrated and previously described, the analyzer apparatus furtherincludes a cartridge assembly for holding the sample processingcartridge, and the configuration processing circuitry and identificationcircuit to identify configuration information for the specific sampleprocessing cartridge. The sample processing cartridge is loaded into thecartridge assembly and in response thereto, the analyzer apparatusconfigures itself for analyzing the specific biological sample. Theconfiguration can include use of the different stimulators and/orinterface tools of the gantry at different times, locations, and/orbased on other interface parameters. As previously described, thestimulators include an optics stimulator, the gantry, an electricalstimulator, pneumatic stimulator, and optionally, additional mechanicalstimulator.

In specific embodiments, the thermal stimulator, or a portion thereof(e.g., the TEC), can be part of the gantry, such as an interface tool ofthe gantry apparatus. The thermal stimulator provides temperaturecontrol at specific locations and times to enable the customized sampleprocessing required by the sample-processing cartridge. The at leastportion of the thermal stimulator (via the TEC) is movable by thegantry. Further, in specific embodiments, the optical stimulatorincludes a mechanical mechanism, such as a wheel that the digitalmicroarray is placed on that rotate and/or that rotates the location ofthe light beam on the digital light beam. Such a mechanical mechanismcan be an interface tool located on the gantry head of the gantry, inspecific embodiments.

FIGS. 7E-7F illustrate a partial view of an analyzer apparatus includinga gantry in accordance with various embodiments. As illustrated by FIG.7E, the cartridge assembly 784 includes a tray that is configured tohold the sample-processing cartridge 783. The tray can move to multiplepositions. For example, the tray can have and/or be moved by theanalyzer apparatus to a first position in which the tray is locatedoutside the analyzer apparatus 780 such that a user can place thesample-processing cartridge 783 within the tray, as illustrated by FIG.7E. FIG. 7F illustrates a second position of the tray in which the trayis enclosed by the analyzer apparatus 780 and the analyzer apparatusconfigures itself for analyzing the biological sample contained therein.As is further illustrated by FIG. 7E-7F, the gantry is mounted to theanalyzer apparatus 780 via brackets (e.g., bracket 755-1 is illustrated)and the gantry head 756 is coupled to a bridge framework and a set oftracks, and located proximal to the second position of the tray of thecartridge assembly 784. The sample-processing cartridge 783 can beloaded into the cartridge assembly 784 such that the top layer thatcontains the reagents module and other modules (e.g., top layer 442illustrated by FIG. 4) is located proximal to the gantry head 756 (e.g.,the top layer is facing upward).

FIGS. 7G-7I illustrated different examples of specific gantryapparatuses, in accordance with various embodiments. The gantriesillustrated by FIGS. 7G-7I can include the structural components used toprovide the functional features as previously described in connectionwith the gantries illustrated by FIGS. 7A-7B, such as the previouslydescribed gantry head having a plurality of interface tools and whichcan be moved to a variety of locations inside and outside of a set ofparallel tracks.

The gantries illustrated by FIGS. 7G-7I can provide the movement of thegantry head using a variety of mechanisms. For example, FIG. 7Gillustrates an example of a gantry apparatus in accordance with variousembodiments. As illustrated, the gantry apparatus includes a set oftracks 765-1, 765-2, a bridge framework 766, a vertical adjustment arm767, and a gantry head 756. The set of tracks 756-1, 756-2 are arrangedparallel to one another and the bridge framework 766 spans the set oftracks. For example, the bridge framework can be perpendicular to theset of tracks, although embodiments are not so limited and the bridgeframework can be at a variety of angles to the set of tracks. Thevertical adjustment arm 767 can be perpendicular to the bridge framework766 and the set of tracks 756-1, 756-2. The vertical adjustment arm 767can couple with the gantry head 756, and can allow the gantry head 756to be moved up or down the length of the vertical adjustment arm (e.g.,to be moved further away from the bridge framework or closer to thebridge framework, respectively), such as along the axis 768. The gantry,in specific embodiments and as further illustrated herein, is enclosedby the analyzer apparatus. The set of tracks can be parallel to oneanother and elongate in a first direction 762, such as along a width ora length of the analyzer apparatus. The bridge framework spans the setof tracks in a second direction 764 and can travel along the set oftracks in the first direction 762 that the set of tracks elongate in.

The gantry head 756 includes the plurality of interface tools arrangedthereon. The gantry head can provide a particular physical interactionwith the biological sample by rotating the gantry head to align arespective interface tool with a particular location, as furtherdescribed herein. In specific embodiments, the gantry moves the gantryhead to different locations that are between and outside the set oftracks in two-dimensional and/or three-dimensional directions (e.g., Xand Y and/or X, Y, and Z) via movement of the bridge framework and/organtry head. The different interface tools can include a thermal energytool to heat or cool the biological sample (e.g., a TEC), a magneticsource to apply magnetic forces, an acoustic tool for applying acoustictools, a motor, and various other tools.

FIG. 7H illustrates another example of a gantry apparatus in accordancewith various embodiments. As illustrated, the gantry apparatus includesa first set of tracks, a bridge framework 769, a vertical adjustment arm770, and a gantry head 756. The first set of tracks are arrangedparallel to one another and the bridge framework 769 spans the set oftracks. For example, the bridge framework 769 can be perpendicular tothe first set of tracks, although embodiments are not so limited and thebridge framework can be at a variety of angles to the first set oftracks. The bridge framework 769 can include a second set of tracks772-1, 772-2 arranged parallel to one another and perpendicular to thefirst set of tracks, as illustrated. The vertical adjustment arm 770 canbe coupled to the second set of tracks 772-1, 772-2 such that thevertical adjustment arm can move to different locations along the seconddirection 764 of the second set of tracks (e.g., from one side edge ofthe bridge framework to an opposing side edge of the bridge framework).The vertical adjustment arm 770 can also include a third set of tracksthat are arranged perpendicular to both the first set of tracks and thesecond set of tracks, and which allow the coupled gantry head 756 to bemoved up or down the length of the vertical adjustment arm such as alongaxis 768 (e.g., to be moved further away from the bridge framework orcloser to the bridge framework, respectively). The gantry, in specificembodiments and as further illustrated herein, is enclosed by theanalyzer apparatus. The first set of tracks can be parallel to oneanother and elongate in a first direction 762, such as along a width ora length of the analyzer apparatus. The gantry head includes theplurality of interface tools, as discussed herein. The gantry head canprovide a particular physical interaction with the biological sample byrotating the gantry head to align a respective interface tool with aparticular location, as further described herein.

FIG. 7I illustrates another example of a gantry apparatus in accordancewith various embodiments. As illustrated, the gantry apparatus includesa set of tracks, a bridge framework 773, a set of adjustable brackets774-1, 774-2, and a gantry head 756. The set of tracks are arrangedparallel to one another and the bridge framework 773 spans the set oftracks. For example, the bridge framework 773 can be perpendicular tothe set of tracks, although embodiments are not so limited and thebridge framework 773 can be at a variety of angles to the set of tracks.The bridge framework 773 can be adjustable via the adjustable brackets774-1, 774-2, such that the bridge framework 773 is moved up or downalong the axis 768. The gantry head 756 can be coupled to the bridgeframework 773, such that the gantry head 756 can move to differentpositions along the bridge framework 773, such as along the seconddirection 764. Moreover, the set of adjustable brackets 774-1, 774-2 canmove to different positions along the set of tracks, such as along thefirst direction 762. The gantry, in specific embodiments and as furtherillustrated herein, is enclosed by the analyzer apparatus. The set oftracks can be parallel to one another and elongate in a first direction762, such as along a width or a length of the analyzer apparatus. Thegantry head 756 includes the plurality of interface tools, as discussedherein. The gantry head 756 can provide a particular physicalinteraction with the biological sample by rotating the gantry head toalign a respective interface tool with a particular location, as furtherdescribed herein.

FIGS. 8A-8E illustrate examples of sample-processing cartridges, inaccordance with various embodiments of the present disclosure. Thesample-processing cartridge can include a board assembly with aplurality of chambers that are in fluidic connection and that are usedto perform the hybridization of the probes to the targets in the sample,purification, and amplification (and optionally the hybridization of theamplicons to a substrate, such as a microarray), such as the rapid assayapparatus illustrated by FIGS. 8A-8C. In such an apparatus, relevantchambers and/or modules are in fluidic communication so as to pass thebiological sample from one chamber/module to the next for operating onthe biological sample according to the functionality relevant thereto,such as the hybridization to probes, target purification, andamplification. In other embodiments, one or more additional apparatusescan be used to perform the hybridization and amplification processes,such as various thermal cyclers. For example, the biological sample canbe in fluidic movement through a plurality of chambers of asample-processing cartridge.

As illustrated, the sample-processing cartridges have data 804 thereon,e.g., the barcode, radio frequency tag, and/or memory location, which isused to self-configure an analyzer apparatus for assisting in processingthe biological sample contained within the sample-processing cartridge.The data 804 can include or provide a memory location to obtainconfiguration information used to identify various biochemical processesto be performed and the order for performing the biochemical processes,locations of the sample-processing cartridge associated with thebiochemical processes, and various parameters (e.g., temperature,timing, volume, etc.) associated with each of the biochemical processes.As previously described, the sample-processing cartridge canadditionally include a means for a user to configure the test performedthereon, such as a label for the user to mark and/or coded data readfrom the sample-processing cartridge (e.g., a QR code).

In various embodiments, although not necessarily illustrated by FIGS.8A-8E, the sample-processing cartridge can include a location for theanalyzer apparatus to mark and/or otherwise disable thesample-processing cartridge after processing is complete. For example,the analyzer apparatus can change a color of a thermal label or marker,burn a location of the sample-processing cartridge, and/or code data onthe sample-processing cartridge to disable the sample-processingcartridge or otherwise indicate that the sample-processing cartridge hasalready been processed. The marking and/or disablement can prevent ormitigate an additional test from being performed on thesample-processing cartridge. As a specific example, thesample-processing cartridge can include a thermal label or marker. Afterprocessing the cartridge, the analyzer apparatus uses the thermal energytool (or an optical tool) to change a color of the thermal label ormarker. By changing the color, if the same sample-processing cartridgeis inserted back into the analyzer apparatus, the analyzer apparatusrecognizes that the sample-processing cartridge has already beenprocessed and rejects the test (e.g., outputs error message such asindicating cartridge is already processed). As another specific example,after processing the cartridge, the analyzer apparatus burns a portionof the sample-processing cartridge, such as burning the location of thedata so that the data cannot subsequently be read or burning apredetermined location that indicates the cartridge has been processed.The analyzer apparatus can use the thermal energy source or a laser toburn the sample-processing cartridge. In another embodiment, theanalyzer apparatus may recode the data on the sample-processingcartridge after processing the cartridge.

More specifically, FIG. 8A illustrates an example sample-processingcartridge used for analyzing cell free DNA. The sample-processingcartridge includes a plurality of biochemical processing modules thatare self-contained on a board assembly. The board assembly includesfluid chambers and channels for processing a biological sample. In thespecific embodiment illustrated by FIG. 8A, the biochemical processingmodules includes a sample collection module connected to the blood tubecontaining the blood sample (e.g., plasma or serum), DNA isolationmodule, target purification module (which is also referred to herein as“a DNA extraction module”), target selection module, amplificationmodule, and detection module. The sample-processing cartridge furtherincludes the data 804 used to identify the configuration information andto configure the analyzer apparatus for a series of state configurationsfor processing the biological sample. For example, the configurationinformation can include spatial information identifying the locations ofthe respective modules, orders of processing the respective modules,biological-sample stimulators used to process the modules, and interfaceparameters at different times throughout the analysis.

FIG. 8B illustrates an example of a board assembly and FIG. 8Cillustrates the separate biochemical processing modules. In variousembodiments, the same board assembly can be used to form differentsample-processing cartridges by connecting the respective biochemicalprocessing modules used for processing the biological sample.

FIGS. 8D-8E illustrate other examples sample-processing cartridges. FIG.8D illustrates an example cartridge used to analyze genomic DNA. Thecartridge can include a swab elution module, a lysis module, a reversetranscription and PCR module, and detection module. FIG. 8E illustratesan example cartridge used to analyze mRNA. The cartridge can include aspore extraction module, purification module, PCR module, and detectionmodule.

Embodiments are not limited to the sample-processing cartridgesillustrated by FIGS. 8A-8E and can include a variety of commerciallyavailable cartridges, such as various microfluidic chips.

More Specific/Experimental Embodiments

Embodiments in accordance with the present disclosure include use of ananalyzer apparatus to analyze and/or otherwise process differentsample-processing cartridges. The analyzer apparatus isself-configurable for a plurality of different types of biologicalsamples, mitigating manual configuration by a user, such as a laboratorytechnician, and which allows for the analyzer apparatus to be used for avariety of different analyses and processes. The differentsample-processing cartridges can have different biochemical processingmodules at different locations used to process different types ofbiological samples, such as genomic DNA, cfDNA, synthetic DNA, mRNA,miRNA, and other types of samples. The analyzer apparatus can be used invarious experimental and/or more specific embodiments to analyze aspecific biological sample contained within a specific sample-processingcartridge.

FIG. 9 illustrates an example method of using an analyzer apparatus forperforming an analysis on a biological sample, in accordance withvarious specific and/or experimental embodiments of the presentdisclosure. A biological sample is collected from an organism, such as ahuman or other animal (although embodiments are not so limited and caninclude plant based samples) and placed in a sample-processingcartridge, at 950. The sample-processing cartridge can be configured fora particular analysis, at 956. For example, a plurality of differentsample-processing cartridges can be available and used for differentanalysis. The user selects the particular sample-processing cartridgebased on the process to be performed (e.g., end result intended). Aspreviously described, the sample-processing cartridge can have datathereon that identifies the sample-processing cartridge. In variousembodiments, the data can be used to automatically (e.g., withoutadditional user input) configure the analyzer apparatus for the specificanalysis to be performed. In other embodiments, the user may enter thedata into the analyzer apparatus and/or external processing circuitry incommunication with the analyzer apparatus and which is used toself-configure the analyzer apparatus.

As a specific example, the sample-specific configuration can includeplacing the sample-processing cartridge into the portable container ofthe analyzer apparatus, at 951. In response thereto, the analyzerapparatus identifies the data on the sample-processing cartridge andassociated configuration information, at 953. Using the configurationinformation, the analyzer apparatus can self-configure itself for theparticular analysis including the series of state configurations asdescribed above, at 955.

Using the series of state configurations, an analysis of the biologicalsample is performed. FIG. 9 illustrates a specific analysis of DNA. Forexample, the series of configuration states can include DNA preparationat 959, library preparation at 960, detection at 968, and analysis at974.

The DNA preparation at 959 can include DNA extraction at 957 and DNAisolation at 958 (e.g., lysis and bind). In a specific experimentalembodiment, DNA extraction includes mixing the biological sample withenzymes and chemicals to release the DNA bound to proteins in thesample. In DNA extraction, example processing techniques involve the useof proteinase K, a detergent (such as tween-20), and/or chaotropic salts(such as guanidinium thiocyanate) and heat to activate the proteinase K.In accordance with various embodiments, the analyzer apparatus isconfigurable to engage a reagent block on the sample-processingcartridge (utilizing the gantry), to release liquid extraction reagents(utilizing the pneumatic stimulator), and move the sample to anextraction module (using the pneumatic stimulator). In the case ofextraction, the gantry provides heat through the thermal stimulator(e.g., TEC) to the sample mixed with extraction chemistry to 56 degreesCelsius for 30 minutes and then cools the sample back to roomtemperature to move on to the purification step.

Once the DNA is extracted from bound proteins, the DNA is isolated fromthe rest of the plasma components (proteins, small molecules, lipids,etc.). Various approaches to DNA isolation include the use of silicafrit spin columns or silica coated magnetic beads. In these approaches,the DNA can be bound to the silica frit by adjusting a chaotropic saltconcentration while other biomolecules remain in solution. The DNA isisolated by washing with buffers (e.g. ethanol, isopropanol, lowchaotropic salt buffers) to remove the biomolecules in solution.Finally, the DNA is eluted using a water buffer (e.g. Tris). Inaccordance with the present disclosure, the DNA is isolated using amixing and binding chamber and a series of states as defined by thesample-processing cartridge at the sample run start. In one example, thesample-processing cartridge contains a mixing station and an embeddedsilica frit. The hardware state configures the pneumatic stimulator todeliver X M of guanidinium thiocyanate and Tween 20 to a finalconcentration of 5% to the biological sample in the mixing station(collectively the binding buffer). The mixing can be controlled by theanalyzer apparatus using a number of different biological-samplestimulators: (1) creating turbulent flow using air bubbles (accomplishedby the pneumatic stimulator), (2) the gantry can move a magnet aroundthe chamber with magnetic beads in the chamber or (3) the gantry can usea motor to turn a paddle that is part of the mixing module. Thebiological sample and binding buffers are then flowed over a silicafrit. The DNA is bound under conditions that are used commonly and wellknown by one of ordinary skill in the art. The frit is washed and thendried. The process of drying involves setting states that drive both airflow over the fit and heating from a TEC on the gantry. The biologicalsample is eluted using a Tris EDTA buffer. The gantry and thermalstimulator (e.g., thermal energy tool) provide variable elutiontemperatures to improve the yield of nucleic acid release of the DNA.The description above provides one example workflow of DNA isolation. Aspreviously described, the DNA preparation can include one module or twoseparate modules used to respectively perform the extraction andisolation.

The library preparation, at 960, can include adding probes to thesample, at 961, and binding the probes to target DNA (e.g.,hybridization), at 963. The probes, as would be appreciated, can becomplementary to target sequences. The probes can be configured to bindto detection probes which may be bound to an array. For example, thedetection probes can include a complementary sequence to the probes. Asfurther described herein, in some embodiments, streptavidin solidssupports are used to enable the capture of specific targets. The targetsbound to the probes can then be ligated, at 965. For example, probesthat annealed to the sample DNA are ligated together joining two probesthat were previously independent molecules so that a single moleculeincludes both universal primer binding sites. The analyzer apparatus canprovide pressure, flow control, magnetic forces, and heating, such asvia the gantry and/or use of other biological-sample stimulators.

The bound targets are then amplified via a PCR process, at 967. Duringthe amplification step, the analyzer apparatus can change configurationto provide hardware components to the location defined by theconfiguration processing circuit for amplification and controls thetiming at each temperature state. In various embodiments, the PCRprocess includes universal PCR that uses universal PCR primers. As aspecific example of a PCR process, the enzyme polymerase anddeoxynucleoside trisphosphates (dNTPs) are added to the sample.Polymerase, such as Taq polymerase, is an enzyme that synthesizesnucleic acid molecules from deoxyribonucleotides. The dNTPs are thebuilding blocks, e.g., the deoxyribonucleotides, from which polymerasesynthesizes new DNA and/or RNA strands. Other components and reagentsmay be added, such as a buffer solution to provide a chemicalenvironment that is suitable for activity and stability of polymerase,bivalent cations, magnesium, manganese ions, and/or potassium ions. Thevarious components and/or reagents are added to the sample via movementof the biological sample through one or more chambers of thesample-processing cartridge, although embodiments are not so limited andcan include the addition of components and/or reagents through othertechniques.

The example PCR process includes repeated cycles of temperature changes.The cycling includes denaturation, annealing, and elongation. Denaturingcan include heating the reaction to a first threshold temperature (e.g.,94-98 degrees Celsius) for a period of time, such as 20-30 seconds. Suchdenaturing causes nucleic acid melting by disrupting the hydrogen bondsbetween complementary bases and results in single-stranded nucleic acidmolecules. The annealing operation can include heating the reaction to asecond threshold temperature that is lower than the first thresholdtemperature (e.g., 50-65 degrees Celsius) for a period of time, such as20-40 seconds. Such annealing causes the PCR primers to bind (e.g.,anneal or hybridize) to the target. The elongation can include heatingthe reaction to a third threshold temperature which is dependent on theparticular polymerase used, whether Taq polymerase or another suitablethermostable DNA polymerase. Using Taq, this polymerase can be optimallyactive at a temperature of 75-80 degrees Celsius and a temperature of 72degrees may be used. During the elongation process, polymerasesynthesizes a new nucleic acid strand complementary to the target byadding dNTPs that are complementary to the target in 5′ to 3′ direction,and condenses the 5′-phosphate group of the dNTPs with the 3′-hydroxylgroup at the end of the nascent (extending) nucleic acid strand.

After the repeated cycles, a final elongation is performed. The finalelongation includes heating the reaction to a fourth thresholdtemperature (e.g., 70-74 degrees Celsius or a value less than 90 degreesCelsius) for a period of time, such as 5-15 minutes. The finalelongation process is used to ensure any remaining single-strandednucleic acid sequence is fully extended. Optionally, after the finalelongation, a final hold is performed. The final hold includes coolingthe reaction to a particular temperature (e.g., 4-15 degrees Celsius).In various embodiments, the amplified reaction is stored within at theparticular temperature. For example, the biological sample can beprocessed by the analyzer apparatus for subsequent analysis. In otherspecific embodiments, the amplicons are not stored, but rather analyzedimmediately after the amplification process using the analyzerapparatus. As previously described, the library preparation can includeone module or separate modules used to respectively perform the targetselection and amplification. The gantry, thermal stimulator, andpneumatic stimulator (as well as the electrical stimulator) can be usedto provide the various interactions described above, including therepeated cycles of temperature changes.

The amplicons are bound to the substrate, such as an array. The targetscan be detected at 968 via post-PCR processing at 969, purification at971, and detection at 973, such as via a detection module as previouslydescribe. Various post-PCR processing can be performed includingpurification and detection at 968. In various embodiments, an analysisis done by hybridization to a substrate, such as a microarray. Theanalyzer apparatus controls the mixing of the sample and hybridizationbuffer in preparation for DNA hybridization using the pneumaticstimulator. In addition, the analyzer apparatus can control the opticaland thermal stimulators. The protocol (e.g. hybridization time,temperature, imaging time, mixing) is defined by the sample-processingcartridge prior to the run and the analyzer apparatus is configured atthe moment.

In some specific embodiments, the output can include an analysis of thequantification of targets, at 974. For example, a digital output isprovided by analyzing the surface of the substrate. Fluorescent signalsat unique locations of the substrate, and indicative of a tag sequenceand associated target, are analyzed and/or imaged using the opticalstimulator, at 975. The fluorescent signals are referred to as tagsignals in FIG. 9. In response to detecting a tag signal, the intensityof the tag signal is background corrected using a background noise valueand normalized, at 977. In various embodiments, the background correctedand normalized tag signal is compared to a threshold to convert theoutput to a digital result (e.g., 0 or 1, pass/fail, off/on) for eachtag indicative of a target at, 979. The threshold includes a simplepass/fail threshold. Optional, the binary result is output for eachunique location that is associated with a tag sequence indicative of atarget being analyzed, at 981, the binary results are combined, at 982,and the target count scores are output, at 983. For more generalinformation regarding quantifying targets and specific informationrelating to a digital output of quantified targets, references is madeto PCT Application (Ser. No. PCT/US2017/024098), entitled “Apparatusesand Methods for Assessing Target Sequence Numbers,” filed Mar. 24, 2017,which is fully incorporated herein by reference. Although embodimentsare not limited to a digital output and can include a variety ofsubstrate analyses.

FIG. 10 illustrates an example method of using an analyzer apparatus forperforming an analysis on a biological sample, in accordance withvarious embodiments of the present disclosure. For example, FIG. 10illustrates an example of analyzing cell free (cf)DNA in accordance withvarious specific and/or experimental embodiments. As illustrated cfDNAanalysis can include DNA extraction at 1001, DNA isolation at 1003,biotinylation at 1005, probe anneal at 1007, ligation and streptavidinbinding at 1009, universal PCR at 1011, quantification of targets at1013, and analysis at 1015.

In some specific and experimental embodiments, the sample-processingcartridge illustrated by FIG. 8A is inserted into an analyzer apparatusillustrated by FIG. 2 which has a gantry as illustrated by 7A. As may beappreciated, embodiments are not so limited and a variety ofsample-processing cartridges and analyzer apparatuses can be used. Inresponse to insertion of the sample-processing cartridge illustrated byFIG. 8A into the analyzer apparatus, the sample-specific configurationcircuitry of the analyzer apparatus (e.g., sample-specific configurationcircuitry 218 illustrated by FIG. 2) identifies the data (e.g., data 804illustrated by FIG. 8A) located on the sample-processing cartridge anduses the data to configure itself. The self-configuration includes aseries of state configurations, as previously described, includingidentification of which biological-sample stimulators interact with thebiological sample at particular times, as well as the positions in theportable container for the biological-sample stimulators at thedifferent times. The positions are associated with locations of thebiochemical processing modules of the sample-processing cartridge. Thedata on the sample-processing cartridge provides spatial locationinformation of the specific biochemical processing modules (e.g., thepurification, DNA isolation, target selection, amplification, anddetection modules) self-contained in the sample-processing cartridgealong with timing and or temperature information and identification ofthe selected biological-sample stimulators used for performing theanalysis at the specific times.

The identified positions are used by the different biological-samplestimulators to interact with the biological sample at the correctlocations of the sample-processing cartridge. In some embodiments, thepneumatic stimulator (e.g., pneumatic stimulator 222 illustrated by FIG.2) can use the identified positons to send forces that control movementof the sample throughout the analysis or cause specific channels to beblocked using a pneumatic valve. As previously described, the pneumaticstimulator includes a pump, tubing and channels that sends forces towardthe biological sample and constantly controls movement of the biologicalsample through the sample-processing cartridge based on theconfiguration information. The gantry can locate different interactivetools at any locations within the analyzer apparatus. More specifically,the gantry head is moved in x, y, and/or z directions to the differentpositions and based on identification of locations of the differentbiochemical processing modules of the inserted sample-processingcartridge.

As previously described, the sample-processing cartridge includes aplurality of biochemical processing modules. In an example experimentalembodiment, the sample-processing cartridge includes, as illustrated byFIG. 8A, a purification module used to perform DNA preparation includingDNA extraction at 1001 and DNA isolation at 1003, a target selectionmodule and amplification module used to perform library preparationincluding (optionally) biotinylation at 1005, probe anneal at 1007,streptavidin binding and ligation at 1009 and universal PCR at 1011, anda detection module used to quantify targets at 1013 and analyze thetargets at 1015. Each biochemical process module can include at leastone chamber that is connected to other portions of the biochemicalprocessing module (or other modules) by channels and valves. Thepneumatic stimulator controls the flow of the biological sample andother reagents through the sample-processing cartridge. In the specificexperimental embodiment, the purification module includes a lysischamber, binding elements (e.g., beads or solid supports), a mixingchamber, and a TEC interface. The DNA isolation chamber can include oneor more binding agent chambers configured to hold liquid reagents andselectively provide the reagents to chambers of the purification module.The target selection module can include one more chambers, lyophilizedprobes and enzymes, and a TEC interface. In specific embodiments, thetarget selection module includes a biotinylation chamber, a probechamber, and a ligation chamber. In other embodiments, the targetselection module includes a single library preparation chamber used toperform the library preparation. The amplification module includes anamplification chamber, lyophilized primers, enzymes and other reagents,and one or more TEC interfaces. The detection module includes a mixingchamber to prepare the biological sample for hybridization, ahybridization chamber having an assay, and interfaces to the TEC,optics, and laser.

The DNA extraction 1001 and DNA isolation 1003 can be used to performDNA preparation. DNA preparation can be performed using multiple modulesor a single module of the sample-processing cartridge. For example, asillustrated by FIG. 8A, the DNA extraction module is separate from theDNA isolation module. Although embodiments are not so limited and apurification module (e.g., such as the purification module 334illustrated by FIG. 3) can be used to perform both DNA extraction andisolation. After inserting the sample-processing cartridge into theanalyzer apparatus and configuring for analysis, the pneumaticstimulator moves at least a portion of the biological sample from ablood tube (or other input for the biological sample) to the one or moremodules for DNA preparation. In a specific example, the pneumaticstimulator moves the portion of the biological sample from the bloodtube to the purification module for DNA extraction followed by DNAisolation. For example, and as further described in the below specificexperimental embodiment, 2 mL of plasma can be moved from a blood tubecontainer that is holding 2.7 mL of plasma.

As previously described, DNA extraction at 1001 involves mixing rawplasma with enzymes and chemicals to release the cfDNA bound to proteinsin the plasma within the purification module of the sample-processingcartridge. For DNA extraction, the pneumatic, electrical, and mechanicalstimulators can be used. Typical processing techniques involve the useof proteinase K, a detergent (such as tween-20), and/or chaotropic salts(such as guanidinium thiocyanate) and heat to activate the proteinase K.In accordance with various embodiments, the analyzer apparatus isself-configurable to engage a liquid reagents module on thesample-processing cartridge (utilizing the gantry), to release liquidextraction reagents (utilizing the pneumatic stimulator), move thebiological sample to the purification module (using the pneumaticstimulator), and mix solutions (using the magnetic or mechanicalelements of the gantry, or the pneumatic stimulator). The purificationmodule can include a mix chamber used for mixing the liquid extractionreagents with the biological sample. In some embodiments, the mixchamber has proteinase K located therein, and the detergent and/orchaotropic salts are released from the liquid reagents module (e.g.,such as from a liquid reagents module 338 illustrated by FIG. 3) andmoved to the purification module via use of the pneumatic stimulator. Inother embodiments, each of the liquid extraction reagents, includeproteinase K, are moved from the liquid reagents module. The gantryprovides heat through the thermal stimulator (e.g., the TEC) to thebiological sample mixed with extraction chemistry to 56 degrees Celsiusfor 30 minutes and then cools the biological sample back to roomtemperature to move on further processing and purification. For example,the gantry moves the gantry head in an x, y, and/z direction to positionthe gantry head and a respective heat source at a location of orassociated with the purification module and provides the heat (e.g., 56degrees Celsius) for the respective amount of time and at the particulartime.

Once the DNA is extracted from bound proteins, at 1003, the DNA isisolated from the rest of the plasma components (proteins, smallmolecules, lipids, etc.). As noted above, a DNA isolation module can beused to perform DNA isolation. The DNA isolation module includesdifferent liquid reagent chambers and/or bead elements. For example, thebiological sample, which includes the extracted DNA mixed with theliquid extraction reagents, is moved from the mix chamber to one or moreother chambers for isolating the DNA (e.g., mixing and/or bindingchambers which are part of the purification module). The biologicalsample with liquid extraction reagents is moved via the pneumaticstimulator. While, after, and/or before moving the biological sample,the gantry can also move the gantry head to a position near the otherchambers by moving the gantry head in an x, y, and/or z direction. Welldescribed approaches to DNA isolation include the use of silica fritspin columns or silica coated magnetic beads. In these approaches, theDNA is preferentially bound to the silica by adjusting a chaotropic saltconcentration while other biomolecules remain in solution. The DNA isisolated by washing with buffers (e.g. ethanol, isopropanol, lowchaotropic salt buffers) to remove the biomolecules in solution.Finally, the DNA is eluted using a water buffer (e.g. Tris).

In a specific experimental example, the purification module contains a(binding) chamber having an embedded silica frit. Although embodimentsare not so limited and other types of binding elements can be used. Thestate configurations can include the pneumatic stimulator delivering X Mof guanidinium thiocyanate (GTC) and Tween 20 to a final concentrationof 10% to the biological sample in the mixing chamber (collectively, thebinding buffer). In the above-described specific embodiment, thesolution of plasma and proteinase K are mixed with isopropanol andadditional GTC and then flowed to the binding chamber having theembedded silica frit. While in the binding chamber, the solution iswashed with different buffers (wash and ethanol), then dried and elutedusing the elution.

The mixing can be controlled by the analyzer apparatus using a number ofdifferent biological-sample stimulators to: (1) create turbulent flowusing air bubbles (accomplished by the pneumatic stimulator), (2) thegantry can move a magnet around the chamber with magnetic beads in thechamber or (3) the gantry can use a motor to turn a paddle that is partof one or more of the chambers. The gantry head, which may be located ata position associated with the location of the purification module, canrotate to utilize different interface tools used to provide differentinteractions with the biological sample. The biological sample andbinding buffers are then flowed over a silica frit. The DNA is boundunder conditions that are used commonly and well known by one ofordinary skill. The frit is washed and then dried. The process of dryinginvolves setting states that drive both air flow over the frit using thepneumatic stimulator and heating from a TEC on the gantry using a heatsource (e.g., rotating the gantry head to position the heat sourcerelative to the frit). Finally, the biological sample is eluted using aTris EDTA buffer via the pneumatic stimulator which drives (e.g., air)the buffer to the respective chamber. The mechanical and thermalstimulators provide variable elution temperatures to improve the yieldof nucleic acid release of the DNA. Optionally, embodiments can utilizesolid-phase reverse immobilization (SPRI) to bias the purified DNA forspecific lengths. The pneumatic simulator moves the sample to magneticbeads held in a chamber which mixes the sample with the beads. The beadsare captured using a magnet on the gantry to enable the pneumaticstimulator to empty the chamber of the binding solution and providemultiple solutions of different polyethylene glycol and ethanolpercentages in order to bias the washing of different DNA fragmentlengths. Finally, the gantry stimulator collects the beads while thepneumatic stimulator empties the chamber and introduces an elutionbuffer. The DNA sample is eluted from the bead by a TEC on the gantry asdirected by the data encoded in the consumable cartridge. The DNA isthen moved by the pneumatic simulator to prepare the library fortargeted sequence analysis.

After the DNA preparation, the library can be prepared. Librarypreparation can include use of a target selection module and anamplification module of the sample-processing cartridge. For example,after extracting and isolating the DNA, the biological sample is movedto the target selection module via the pneumatic stimulator. In manytypical library approaches, streptavidin solids supports are used tocapture specific reagents. In the case of cfDNA purification, astreptavidin support can be used to capture the cfDNA after it has beenbiotinylated by a biochemical terminal transferase enzyme, at 1005. Thethermal stimulator and gantry provide the conditions to carry out thebiochemical reaction, while the pneumatic stimulator provides themovement of the biological sample to the biotinylation chamber. Forexample, the biological sample (which has various liquid reagents added)is moved from the purification module to the target selection module.The target selection module includes a biotinylation chamber havingreagents for performing biotinylation, such as biotin and terminaldeoxytransferase. The gantry head can rotate to locate the heat sourceproximal to the biotinylation chamber and to heat the mixture (such asto 37 degrees for sixty minutes).

The solution is then mixed with probes for annealing. After annealingwith probes, at 1007, the mixture containing the biological sample ismoved and captured on a streptavidin solid support in a ligation chambervia the pneumatic stimulator. The target selection module can includethe chamber for performing biotinylation and/or the probe chamber havingthe streptavidin solid support. The solid support can isolate the cfDNAin multiple ways, such as magnetic beads coated with streptavidin orflow through filters functionalized with streptavidin. The ligationchamber can include the solid support and primers, although embodimentsare not so limited and the solid supports and primers can be moved intothe probe chamber to mix with the biological sample. The gantry head,which is located at the target selection module and/or specifically atthe probe chamber can be used to heat the probe chamber (e.g., 70Celsius for 2 minutes and 35 Celsius for 2 hours), and liquid reagentsare brought into the probe chamber from the liquid reagents module 338(such as, LS wash and HS wash) using the pneumatic stimulator 222. Thegantry head can then rotate to locate a magnetic source proximal to theprobe chamber, and uses the magnetic source to mix the different liquidsin the probe chamber.

Next the probes that are annealed to the sample DNA are ligated togetherjoining two probes that were previously independent molecules so that asingle molecule now includes both universal primer binding sites, at1009. In these examples, the analyzer apparatus provides pressure, flowcontrol, magnetic forces, and heating. The ligation can occur by thegantry head providing a series of interactions with the biologicalsample and various liquid reagents. In some embodiments, the targetselection module includes a ligation chamber, although embodiments arenot so limited and one or more of the biotinylation chamber, the probechamber, and ligation chamber are a single chamber. The mixture, whichincludes DNA bound to the streptavidin support (or other solidsupport(s)) and primers) is moved to the ligation chamber using thepneumatic stimulator 222. The gantry head is also moved to a positionassociated with (or already is located at the position) the ligationchamber to provide various interactions with the biological sample. Forexample, the gantry head can heat the biological sample and variousliquid reagents, liquid reagents are brought into the ligation chamberfrom the liquid reagents module 338 (such as, HS wash and elution wash)using the pneumatic stimulator, a magnetic source is used to mix thedifferent liquids in the ligation chamber, the mixture is heated usingthe heat source, and the magnetic source is again used to mix themixture. In the above-described specific embodiment, the solutioncontaining DNA bound to the solid support and probes in the ligationchamber is washed and eluted. Elution can be accomplished chemically(NaOH) or thermally (denaturing the double stranded DNA above theligated product melting temperature).

The mixture is then flowed to the amplification module, which includesan amplification (e.g., PCR) chamber and probes, enzymes and variousreagents. Universal amplification and labeling of the annealedbiological sample utilize both thermal and mechanical stimulators withsample movement controlled by the pneumatic stimulator, at 1011. Duringthe amplification step, the analyzer apparatus changes configuration toprovide the different biological-sample stimulators to the locationdefined by the configuration processing circuit for amplification andcontrols the timing at each temperature state. The amplification caninclude repeated cycles of different temperatures, e.g., PCR, as wouldbe well understood by one of ordinary skill. The gantry head can providethe different temperatures and for the particular amount of time at theamplification chamber. In the above-described specific embodiment, thesolution containing DNA eluted from the solid support is mixed with PCRmixture.

Although the above describes various different chambers used for thelibrary preparation, in some embodiments, the library preparationincudes use of a target selection module and an amplification module.The target selection module includes a first chamber in which thebiological sample (as extracted and isolated) is mixed with a solidstructure, oligonucleotide probes and various reagents to anneal theisolated DNA targets to the solid structures and probes (e.g.,biotinylation, probe anneal, and ligation). Various liquid reagents arebrought to the first chamber via the pneumatic stimulator. Theamplification module includes an amplification chamber, as describedabove, which is used to perform PCR by mixing the bound target DNA witha PCR mixture and performing the amplification using the pneumaticstimulator and gantry.

The amplified DNA targets are then moved to a detection module of thesample-processing cartridge via the pneumatic stimulator for sequenceanalysis. The gantry head can additionally be moved to a positionassociated with the detection module. The sequence analysis can beperformed by hybridization of the targets to a (DNA) microarray. Forexample, the solution is flown to a mixing chamber for preparing thebiological sample for hybridization. The analyzer apparatus controls themixing of the biological sample and hybridization buffer, such as SSPE,in preparation for DNA hybridization using the pneumatic stimulator. Theprepared solution is then flowed to a hybridization chamber that has anassay, such as a microarray, for hybridizing to the assay and fordetection of the targets. The hybridization assay can be heated toassist in the hybridization. The analyzer apparatus can control theoptical and thermal stimulator for performing the hybridization andsubsequent detection. The protocol (e.g. hybridization time,temperature, imaging time, mixing) is defined by the sample-processingcartridge prior to the run and the analyzer apparatus is configured atthe moment which can be used to quantify targets, at 1013, and performanalysis on the results, at 1015. The detection module can include, inthe specific example, a mixing chamber having hybridization buffer andthe hybridization chamber having the (DNA) microarray (althoughembodiments are not so limited), and the pneumatic stimulator is used tomove the mixture from the mixing chamber to the hybridization chamber.

Although the above FIG. 10 describes a particular example, embodimentsare not limited to the specific liquid reagents, chambers, temperatures,and/or amounts of reagents/liquids. The reagents, in further specificembodiments, can be frozen and/or lyophilized.

The following is a specific example of processing a biological sampleusing the analyzer apparatus as illustrated by FIG. 2 in accordance withvarious embodiment and the sample-processing cartridge illustrated byFIG. 8A. In the specific example, the pneumatic stimulator (e.g., thepneumatic stimulator 222 illustrated by FIG. 2) moves 2 mL of thebiological sample from the plasma tube to the purification module forDNA extraction and DNA isolation. For example, 2 mL of plasma is mixedwith 0.58 mL of lysis reagents including proteinase K in the lysischamber and then flowed to a binding chamber. In the binding chamber,the 2.58 mL solution of plasma and proteinase K are mixed with 2.0 mL ofa GTC and tween-20 (forming 4.58 mL solution in the binding chamber) andthen flowed to the mixing chamber having the embedded silica frit. Whilein the mixing chamber, the solution is washed with different buffers(750 uL wash and 750 uL ethanol), then dried and eluted using theelution to form 20 uL of solution. The 20 uL solution is then flowed tolibrary preparation module.

The solution, now 20 uL, is then flown to the target selection module.More specifically, the 20 uL solution is flown to the biotinylationchamber and mixed with 1 uL of biotin and heated to 37 degrees for 60minutes to form a solution of 21 uL. The 21 uL solution is then flown toa probe chamber (or optionally all performed in a single chamber) havingthe streptavidin solid support and probes, and is washed with 75 uL washand 75 uL HS wash to form a solution of 21 uL. The 21 uL solution isthen flown to the ligation chamber (in various optional embodiments, thebiotinylation chamber, the probe chamber, and ligation chamber are asingle chamber). The solution in the ligation chamber is heated to 45degrees Celsius for 30 minutes, liquid reagents are brought into theligation chamber from the liquid reagents module (e.g., the liquidreagents module 338 illustrated by FIG. 3), such as, HS wash and elutionwash, using the pneumatic stimulator, and a magnetic source is used tomix the different liquids in the ligation chamber. The solution is thenheated to 95 degrees for 2 minutes using the heat source, and themagnetic source is again used to mix the solution. The ligation processcan form a solution of 25 uL. The 25 uL solution is then moved to anamplification chamber of the amplification module and PCR is performed.For example, the ligated probes and primers are mixed with 1 uL of PCRmixture to form a 26 uL solution, which is brought through repeatedcycles of different temperatures.

The amplified DNA targets are then flown to the detection module. Forexample, the solution containing the amplified DNA targets is flown tothe mixing chamber of the detection module and mixed with hybridizationbuffer, such as SSPE. The solution is then directed to the hybridizationchamber having the microarray and heated to assist in hybridizationusing the heat source of the gantry. The detection module includesinterfaces for the optical stimulator, such as optic and laserinterfaces, and which are used to detect targets bound to themicroarray.

The above described example is a specific experimental embodiment andvarious embodiments in accordance with the present disclosure caninclude a variety of variations. Some variations, as described above,can include different sample-processing cartridges having differentnumbers or types of biochemical processing modules. Further, thebiochemical processing modules can include different chambers and flowmethods. For example, the reagents can be liquid, solid, frozen and/orlyophilized. The reagents can be located in a chamber of the biochemicalprocessing module and the sample is moved to the chamber. In otherembodiments and/or in addition (at a different biochemical step),reagents can be located in a first chamber of the biochemical processingmodule or the liquid reagents module and can be moved to a secondchamber that the sample is located in. For DNA preparation, othervarious embodiments include combining the lysis chamber with the bindingchamber and/or mixing chamber, combining the binding and mixing chamberinto a single binding chamber, using a bind solution for wash, and/orusing beads as the solid support. Targets that are analyzed are notlimited to cfDNA, and can include gDNA, mRNA, miRNA, and other nucleicacid targets, as well as non-nucleic acid targets, such as synthetic DNAcoupled to an antibody.

FIG. 11 illustrates an example method of using an analyzer apparatus forperforming an analysis on a sample, in accordance with variousembodiments of the present disclosure. For example, FIG. 11 illustratesan example of analyzing cell messenger RNA (mRNA) in peripheralmononuclear cells (PBMCs). The consumable cartridge provides informationto the hardware system, e.g., the configuration processing circuitry asillustrated in FIG. 7D, to enable remote programming of the hardwaresystem states to provide for analysis of mRNA in multiple samples. Theillustrative embodiment described below is for mRNA and can be used todiagnosis infections, inflammatory disease (e.g. lupus), and certaincancers. In such embodiments, a sample of whole blood is lysed toextract the mRNA and other nucleic acids from their cellularcompartments, at 1121. The RNA is isolated from the sample using one ormore of a variety of methods, at 1123, including the solid phaseextraction and poly-A binding for mRNA specific isolation. Otherapproaches well known to those skilled in the art. After the isolation,in some embodiments, the mRNA is separated from the total RNA whichincludes both tRNA and rRNA, at 1125.

One example approach to mRNA purification is using a capture probelabeled with a separation molecule (e.g. biotin), as shown in FIG. 12,which is subsequently bound to a solid support using a streptavidininteraction. The capture probe can be designed to cover splice junctionsor can be a poly-T nucleic acid that hybridizes to the poly-A tail thatis unique to mRNA transcripts. The hybridized DNA probe: RNA targetbinds to a solid support using the separation molecule interactionswhile the remaining nucleic acids are washed away. In embodiments thatthe capture probe is a poly-T oligonucleotide, (all) the mRNA arecaptured and the analyzer apparatus and analysis software can supportdevelopment applications. In the instance where the capture probe is forspecific transcripts, the resulting analysis may be only for thosespecific transcripts.

Once the mRNA is captured, at 1127, in specific embodiments, analysisprobes are annealed to the remaining transcripts. The analysis probesare designed to specifically target different mRNA transcripts. In someembodiments, only a single analysis probes set may target a specifictranscript sequence or multiple different analysis probes can be used toprovide a signal amplification. The target probes contain universal PCRprimers and tag sequences for analysis on a DNA microarray. The analysisprobes are linked using a ligase.

FIG. 12 illustrates a ligase that is active on DNA:RNA hybrid, inaccordance with various embodiments. However, embodiments are not solimited and other embodiments can include converting the mRNA transcriptto complementary DNA using a reverse transcriptase and then usingstandard DNA:DNA ligase to link the two analysis probes, such as at1129.

After ligation, e.g., at 1129, is complete the analysis probes areseparated from the target transcript using one or more of multiplemethods. In one example method, heating the solution above the meltingtemperature of the ligated analysis probe can elute the probe from thesolid support and the transcript. As described above in the cfDNAimplementation, the ligated probes are amplified together in singlereaction pool based on the universal primers, at 1131.

The amplified DNA targets are then flown to the detection module. Forexample, the solution containing the amplified DNA targets is flown tothe mixing chamber of the detection module and mixed with hybridizationbuffer, such as SSPE. The solution is then directed to the hybridizationchamber having the microarray and heated to assist in hybridizationusing the heat source of the gantry. The detection module includesinterfaces for the optical stimulator, such as optic and laserinterfaces, and which are used to detect targets bound to the microarrayfor quantifying the targets 1133 and further analysis at 1135 aspreviously described.

Various embodiments are implemented in accordance with patent documentsas previous described and identified, and which are fully incorporatedby reference. For information regarding details of these and otherembodiments, applications and experiments (as combinable in varyingdegrees with the teachings herein), reference may be made to theteachings and underlying references provided in the patent documentswhich form part of this patent document and is fully incorporatedherein. Accordingly, the present disclosure is related to methods,applications and devices in and stemming from the disclosures in thepatent documents and also to the uses and development of devices andprocesses discussed in connection with the references cited herein.

Certain embodiments are directed to a computer program product (e.g.,nonvolatile memory device), which includes a machine orcomputer-readable medium having stored thereon instructions which may beexecuted by a computer (or other electronic device, such as processingcircuitry or the detection circuitry) to perform theseoperations/activities.

Various embodiments described above may be implemented together and/orin other manners. One or more of the items depicted in the presentdisclosure can also be implemented separately or in a more integratedmanner, or removed and/or rendered as inoperable in certain cases, as isuseful in accordance with particular applications. In view of thedescription herein, those skilled in the art will recognize that manychanges may be made thereto without departing from the spirit and scopeof the present disclosure.

Based upon the above discussion and illustrations, those skilled in theart will readily recognize that various modifications and changes may bemade to the various embodiments without strictly following the exemplaryembodiments and applications illustrated and described herein. As anexample, the processing circuitry and the detection circuitry can bepart of separate devices and in communication via a wireless or wiredlink or can be part of the same device. Such modifications do not departfrom the true spirit and scope of various aspects of the invention,including aspects set forth in the claims.

What is claimed is:
 1. A sample-processing cartridge comprising: a boardassembly with fluid chambers and channels configured and arranged forprocessing a biological sample therein; an input port configured andarranged to receive the biological sample; a plurality of biochemicalprocessing modules that are coupled to the board assembly and in fluidiccommunication with the fluid chambers and channels, the biochemicalprocessing modules being configured and arranged to perform biochemicalprocessing on the biological sample; and data located on thesample-processing cartridge configured and arranged to provideconfiguration information specific to the sample-processing cartridge,the configuration information for configuring an analyzer apparatus toperform the biochemical processing using the plurality of biochemicalprocessing modules.
 2. The sample-processing cartridge of claim 1,wherein the sample-processing cartridge comprises multiple layers; themultiple layers including a top layer, bottom layer, and a laminatelayer; the top layer comprising a liquid reagents module; the bottomlayer comprising the plurality of biochemical processing modules; andthe laminate layer comprising fluid channels, valves, and vents.
 3. Thesample-processing cartridge of claim 2, wherein the sample-processingcartridge is configured to be pierced by the analyzer apparatus; theanalyzer apparatus responsive to a placement of the sample-processingcartridge in a cartridge assembly of the analyzer apparatus, theplacement of the cartridge in the cartridge assembly resulting in aliquid communication between the liquid reagents module and one or moreother modules and/or the fluid chambers of the board assembly; and theliquid reagents module containing reagents for processing the biologicalsample.
 4. The sample-processing cartridge of claim 1, wherein the dataon the sample-processing cartridge includes a barcode or radio frequencytag; the barcode or radio frequency tag stores the configurationinformation specific to the sample-processing cartridge, or identifies amemory location of the configuration information.
 5. Thesample-processing cartridge of claim 1, wherein the data on thesample-processing cartridge includes identification of a link; the linkindicative of a cloud-based location providing the configurationinformation.
 6. The sample-processing cartridge of claim 4, wherein theconfiguration information identifies: biochemical processes to beperformed, an order for performing the biochemical processes, a locationof the sample-processing cartridge, or parameters including temperature,time, and volume of each of the biochemical processes to be performed.7. The sample-processing cartridge of claim 3, wherein thesample-processing cartridge further comprises a location for theanalyzer apparatus to disable or mark as disabled the sample-processingcartridge after processing is complete.
 8. The sample-processingcartridge of claim 7, wherein at the location the analyzer apparatuschanges a color of a thermal label or marker, burns the location, orcodes data at the location indicative of the sample-processing cartridgehaving already been processed.
 9. The sample-processing cartridge ofclaim 3, wherein the plurality of biochemical processing modules furthercomprises a purification module, a target selection module, anamplification module, and a detection module.
 10. The sample-processingcartridge of claim 9, wherein the purification module extracts targetsfrom within the biological sample by mixing the biological sample withenzymes or chemicals to release a target from the biological sample;wherein the target includes DNA, RNA, or antibodies.
 11. Thesample-processing cartridge of claim 10, wherein the purification moduleincludes a proteinase K (PK) chamber that contains PK, and a TECinterface for engagement with a TEC.
 12. The sample-processing cartridgeof claim 9, wherein the purification module includes a binding chamber,one or more binding elements, and a TEC interface to allow forengagement with a TEC; wherein the one or more binding elements includebeads or a silica frit.
 13. The sample-processing cartridge of claim 9,wherein the purification module includes two separate modules includingan extraction module and an isolation module, wherein the extractionmodule extracts targets from within the biological sample by mixing thebiological sample with enzymes or chemical to release a target from thebiological sample, the target including DNA, RNA, or antibodies; andwherein the isolation module includes a binding chamber, one or morebinding elements, and a TEC interface for engagement with a TEC, the oneor more binding elements include beads or a silica frit.
 14. Thesample-processing cartridge of claim 9, wherein the target selectionmodule is configured to bind specific targets to probes, the targetselection module including a chamber, probes, enzymes, and a TECinterface.
 15. The sample-processing cartridge of claim 14, whereinspecific targets are isolated from the purification module, the probesare mixed with the isolated specific targets, and the isolated specifictargets are annealed to the probes.
 16. The sample-processing cartridgeof claim 9, wherein the amplification module is configured to amplifytargets bound to probes via a PCR process, the amplification moduleincluding probes, PCR primers, enzymes, and a TEC interface.
 17. Thesample-processing cartridge of claim 16, wherein the target selectionmodule and amplification module are one integral module, the oneintegral module being a library preparation module configured forlibrary preparation; wherein the library preparation includes adding theprobes to the biological sample, and binding the probes to a specifictarget.
 18. The sample-processing cartridge of claim 9, wherein thedetection module is configured to bind amplicons to a substrate anddetect the bound amplicons; wherein the amplicons include a specifictarget bound to a specific probe.
 19. The sample-processing cartridge ofclaim 3, wherein the plurality of biochemical processing modulesincludes a sample collection module used to interface with a biologicalsample container or transfer device, wherein the sample collectionmodule includes a sample chamber configured to hold a volume of thebiological sample.
 20. The sample-processing cartridge of claim 19,wherein the sample collection module is a blood tube.